2

2.

1. Table of Contents

Committees ................................................................................................................................................. 8

Organising Committee .................................................................................................................................... 8
Scientific Committee ....................................................................................................................................... 8
3.

Abstracts....................................................................................................................................................10
Atmospheric correction and fluorescence retrieval over land and water .................................................10
Global Retrievals of Solar-Induced Chlorophyll Fluorescence With TROPOMI .........................................10
FLEX Level-1b to Level-2 data processing chain. Project overview and validation results .......................10
Retrieval of the Sun-Induced Fluorescence in the framework of the FLEX mission .................................11
From proximal sensing to satellite scale: Analyzing and compensating atmospheric effects on oxygenfeatures for retrieving fluorescence..........................................................................................................11
Applications of fluorescence in stress detection .........................................................................................12
Understanding the spectral changes associated to the photoprotection (NPQ) mechanisms ofvegetation: Opportunities for FLEX-FLORIS LR (500-780 nm) products ....................................................12
Active and passive fluorescence measurements under elevated CO2 the field. ......................................13
Calibration and validation of satellite data .................................................................................................13
Radiometric/spectral calibration and co-registration correction algorithms for FLEX/Sentinel-3 Level-2
synergy ......................................................................................................................................................13
Copernicus GBOV service: a support to FLEX products validation ............................................................14
Validation of Sentinel-2 cloud masking and classification products – potential for Sentinel-3 validation?
...................................................................................................................................................................14
Airborne and UAS campaigns .......................................................................................................................15
Collaborative Solar-induced fluorescence measurement campaigns – decsription of objectives, ground /airborne measurements and preliminary results......................................................................................15
Quantitative assessment of Sun-Induced-Fluorescence maps from HyPlant airborne images using
different quality criteria - Part I.................................................................................................................16
UAS-based Chlorophyll Fluorescence Measurements of Barley Canopies – Results from FLEXSense 2018...................................................................................................................................................................16
In situ measurement of fluorescence I ........................................................................................................17
FluoSPECCHIO: A spectral data base system to facilitate a validation network for the upcoming
Fluorescence Explorer (FLEX) mission .......................................................................................................17
Filtering Fluorescence Time Series Acquired with the FloX Monitoring Field Spectrometer for theInvestigation of Vegetation Dynamic Seasonal Trends over Grassland ....................................................18
Retrieval of biophysical parameters from FLEX and Sentinel-3 data .........................................................19
Status on the retrieval models for the traditional biophysical variables (LAI, Cab, fAPAR, FVC and APAR)...................................................................................................................................................................19
Global sensitivity analysis of coupled SCOPE-6S model. ...........................................................................203

Modelling approaches across spatial and temporal scales I .......................................................................21
Investigating diurnal change in spectral reflectance and solar-induced fluorescence to understand non
photochemical activity (NPQ) of Arabidopsis npq mutants ......................................................................21
Downscaling of the solar-induced chlorophyll fluorescence from canopy level to leaf/photosystem level...................................................................................................................................................................21
Sensitivity analyses of forest canopy chlorophyll fluorescence using TLS-reconstructed stands in DART...................................................................................................................................................................22
Modelling approaches across spatial and temporal scales II ......................................................................23
Assimilating satellite SIF into a process-based terrestrial biosphere model: BETHY-SCOPE ....................23
Towards exploiting the carbon constellation of satellite missions: Using a variational data assimilation
approach for a synergistic multi-mission retrieval of bio- and geophysical variables from Sentinel-1 andSentinel-2 data. .........................................................................................................................................23
Forward modelling of Solar Induced Fluorescence from the JULES land surface model..........................24
Fluorescence for aquatic research I-II ..........................................................................................................24
FLEX2018 cruise: preliminary results for the bio-optical characterization of the investigated coastal area
(Tyrrhenian Sea) ........................................................................................................................................24
Retrieval of sun-induced fluorescence in optically complex waters: Insights from observations of theSentinel-3 tandem phase ..........................................................................................................................25
A new SICF retrieval algorithm for water bodies and the implementation possibilities for the FLEX/S3
tandem mission. ........................................................................................................................................25
Analysis of high frequency of remote sensing reflectances in optically complex waters for the next
generation of hyperspectral sensors.........................................................................................................27
Modelling Environmental Impacts And Adaptation On Sustainable Marine Ecosystems In the Gulf-ofGuinea Coast .............................................................................................................................................27
In situ measurement of fluorescence II .......................................................................................................29
Ground-based fluorescence measurements and vegetation dynamics across different ecosystems......29
Chlorophyll Fluorescence Calibration/Validation Measurements at the USDA Beltsville researchcornfield over 20 years ..............................................................................................................................29
Effect of the canopy architecture on the diurnal time course of sun-induced chlorophyll fluorescenceand derived indices ...................................................................................................................................30
Correcting for Sun Induced Fluorescence reabsorption – from leaf to canopy – in chlorophyll-deficientand green soybean plants .........................................................................................................................30
Linking fluorescence and ecosystem processes I - water cycle...................................................................31
The relationship between sun-induced fluorescence and transpiration is determined by atmosphericconditions and less by vegetation properties ...........................................................................................31
Tomography of forest gas exchange: Implications for the development of novel FLEX mission data
products ....................................................................................................................................................31
Investigating the potential of sun-induced chlorophyll fluorescence to advance estimates of ecosystemtranspiration ..............................................................................................................................................32
The mechanistic link between transpiration and sun-induced chlorophyll fluorescence in a mixed forest:
Insights from the 2018 European drought ................................................................................................32
Linking fluorescence and ecosystem processes II - carbon cycle ................................................................33

4

Mechanistic processes driving Sun-Induced Fluorescence and Gross Primary Production under nutrient
manipulation .............................................................................................................................................33
Partitioning the structure and photosynthetic pathway for scaling solar-induced fluorescence to grossprimary production from satellite observations .......................................................................................34
Improvements in GPP spatio-temporal patterns simulated with the ORCHIDEE terrestrial biospheremodel resulting from the assimilation of OCO-2 solar-induced fluorescence products and thedevelopment of a mechanistic SIF model .................................................................................................34
Linking fluorescence and ecosystem processes III ......................................................................................35
Sun-induced chlorophyll fluorescence to understand the responses of terrestrial ecosystem functioning
to climate, environmental changes and extreme events..........................................................................35
Estimating functional diversity using sun-induced fluorescence in terrestrial ecosystems .....................36
Field-scale monitoring of drought stress using chlorophyll fluorescence with the coupled SCOPE-AgroC
model.........................................................................................................................................................37
The effect of heat waves on the physiology and sun induced fluorescence of citrus trees .....................37
Posters ..........................................................................................................................................................39
Is remotely sensed SIF providing information on SIF yield? .....................................................................39
Global retrieval and assessment of terrestrial solar-induced chlorophyll fluorescence from TanSat
satellite measurements .............................................................................................................................39
Comparing satellite observations and measurements from the AtmoFLEX campaign using radiativetransfer calculations ..................................................................................................................................40
Method For Acquiring and Comparing Spatially .......................................................................................40
The evaluation of ecosystem service by satellite-based SIF in South-East Asia........................................41
LASVEG: a combined airborne instrumental platform for simultaneous measurements of laser-induced
fluorescence, SIF, visible reflectance and vertical structure of the canopy ..............................................41
Characterization of sun-induced fluorescence and PRI anisotropy based on field spectroscopy data ....42
Quantitative assessment of Sun-Induced-Fluorescence maps from HyPlant airborne images using
different quality criteria - Part II................................................................................................................42
Linking spatial Fluorescence patterns to soil and atmospheric properties in a heterogeneous agriculture
landscape...................................................................................................................................................43
Mechanistic modeling of leaf gas exchanges expands the utility of SIF into estimation of ecosystemtranspiration ..............................................................................................................................................44
Canopy architectural influence on the interpretation of the biophysical parameters and sun-induced
chlorophyll fluorescence variability: A small-scale laboratory experiment. .............................................44
Measuring sun-induced fluorescence at different scales: Overview over instruments, measurement
setups, protocols and their application at leaf and canopy scale .............................................................45
Temporal upscaling solar-induced chlorophyll fluorescence from the instantaneous to continuous scalecauses an improved correlation with gross primary productivity ............................................................45
Separating physiological from sun-view geometry effects with a high resolution proximal hyperspectral
imager on the Tumbarumba forest flux tower .........................................................................................46
Return of experience from the Sentinel-3 Tandem and lessons learned for FLEX ...................................46
Time series of Sun-Induced Fluorescence, Gross Primary productivity and Transpiration in a
Mediterranean grassland ..........................................................................................................................47
Phenological changes in GOSAT SIF in temperate vegetations in Japan...................................................48
5

Towards field-deployable fluorescing reference targets ..........................................................................48
Validation of atmospheric correction: Collaboration and exchange between Copernicus Sentinel-2 andSentintel-3 teams? ....................................................................................................................................48
Seasonality in solar induced chlorophyll fluorescence and light use efficiency in boreal Finland ...........49
Sun-Induced Fluorescence and Spectral Vegetation Indices for Heterogeneous Ecosystems and Diverse
Peatland Plant Communities .....................................................................................................................49
Can We Measure Sun-Induced Chlorophyll Fluorescence Emitted by Biocrusts? ....................................50
FLUORT: a GUI FLUOresence Retrieval Toolbox for automating and optimizing sun-induced chlorophyll
fluorescence retrieval from spectroscopy data ........................................................................................51
Sun-induced chlorophyll fluorescence: retrievals methods and practical cases for proximal sensing.
Cendrero-Mateo M1, Wineke S2, Damm A3,4, Pinto F5, Alonso L1, Guanter L6, Celesti M7, Sabater N1,
Coglioatti S7, Julitta T8, Goulas Y9, Asen H10, Pacheco-Labrador J11, Mc rthur A12 ..............................52
Instrumental considerations in the proximal sensing of sun‐induced chlorophyll fluorescence .............52
Instrumental characterization, measurements protocols, and retrievals methods in the proximal
sensing of sun‐induced chlorophyll fluorescence .....................................................................................53
Litchfield Savanna Supersite – A CEOS Land Process Validation site in northern Australia .....................53
Adapting the FLEX Fluorescence retrieval concept from land vegetation to inland water ......................546

7

2. Committees

Organising Committee
•
•
•
•
•

A. Damm (UZH, Eawag)
S. Mecklenburg (ESA)
D. Schuettemeyer (ESA)M. Drusch (ESA)
V. Boccia (ESA)

Scientific Committee
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•

Ludovic Bourg (ACRI France)
Astrid Bracher (AWI, Germany)
Fernando Camacho EOLAB Spain
Roberto Colombo (UNIMIB)
Alexander Damm (University of Zurich)
Christian Frankenberg (Caltec, CA) (TBC)
Robert Frouin (SCRIPPS Institution of
Oceanography, US)
Darren Ghent, University of Leicester, UK
Claudia Giardino (CNR, Italy)
Sven Gilliams (VITO Belgium)
Nadine Gobron (JRC, Ispra, Italy)
Yves Goulas (LMD)
Luis Guanter (GFZ-Potsdam, Germany)
Betsy Middleton (NASA)
Franco Miglietta (CNR)
Gina Mohammed (P&M Technologies)
José Moreno (University of Valencia)
Matti Möttus (VTT Technical ResearchCentre of Finland)
Ladislav Nedbal (FZ-Juelich, Germany)
Daniel Odermatt (Eawag, Switzerland)
Uwe Rascher (FZJ)
Christian van der Tol (University ofTwente)8

9

FLEX Level-1b to Level-2 data processing chain.
Project overview and validation results

3. Abstracts

Vicent J1, Matot G1, Hillairet E1, Berthelot B1, Ruiloba
R1, Ruiz-Verdú A2, Sabater N2, Cogliati S3, Verrelst J2,Magnani F5, Santer R1, Moreno J2, Drusch M4
1Magellium, 2Image Processing Laboratory, Universityof Valencia, 3Università degli Studi di Milano-Bicocca,
4ESA/ESTEC, European Space Agency, 5Università di
Bologna
ESA’s FLEX/Sentinel-3 tandem mission aims at mapping
Sun-induced fluorescence (SIF) as a proxy to quantify
photosynthetic activity of terrestrial vegetation. Due tothe complexity of the mission concept and stringent
requirements for the data processing algorithms, ESA
developed an End-to-End Mission Performance
Simulator (E2ES) tool to reproduce the expectedmission performance and consolidate the whole dataprocessing chain.
The development and optimization of the Level-2 dataprocessing chain plays an important role in the
preparatory activities for the future Ground Segment
development. An on-going 2-years ESA/ESTEC project
aims at developing this Level-2 processing chain for its
integration and validation into the FLEX E2E simulator.
The L2 data processing chain consists in four modules:
L2A: creating a synergistic product by co-registering andcross-calibrating FLORIS (FLEX) and OLCI/SLSTR(Sentinel-3) instruments,
L2B: characterizing the atmospheric state (water vapor
and aerosol optical properties) and inverting thesurface apparent reflectance for all mission
instruments,
L2C: retrieving SIF emission from terrestrial vegetation
by a state-of-the-art spectral fitting method, andL2D: determining vegetation biophysical parameters for
a complete interpretation of the SIF signal.

Atmospheric correction andfluorescence retrieval overland and water

Global Retrievals of Solar-Induced Chlorophyll
Fluorescence With TROPOMI

Köhler P1, Frankenberg C1,2, Magney T1, Guanter L3,

Joiner J4, Landgraf J5
1
Caltech, 2JPL, 3German Research Center for
Geosciences (GFZ), 4NASA Goddard Space Flight Center,5
SRON Netherlands Institute for Space Research
The recently launched TROPOspheric Monitoring
Instrument (TROPOMI) is designed to monitor
atmospheric trace gases and air pollutants with anunprecedented resolution in space and time. In
addition, TROPOMI’s spectral coverage, resolution andradiometric accuracy also permit us to retrieve solarinduced chlorophyll fluorescence (SIF) in both red andfar-red wavelength. In this contribution, we will present
our retrieval approach along with the lessons learned
from the first year of TROPOMI SIF data. TROPOMI's
notable radiometric performance in combination with
its wide swath (allowing for almost daily surface
coverage), and ground pixel size of about 7 km x 3.5 km(at nadir) largely outperforms previous and existing
capabilities for a spatial continuous monitoring of SIF
from space. However, interpretation requires caution,
as the broad range of viewing-illumination geometries
covered by TROPOMI’s 2,600-km-wide swath needs tobe taken into account. We will further present anintersensor comparison with OCO-2 (Orbiting Carbon
Observatory-2) SIF, showing excellent agreement andunderscoring the high quality of TROPOMI’s SIF
retrievals.

The FLEX L1B to L2 Algorithms Development study isleaded by Magellium (France) with the universities ofValencia (Spain), Bologna and Milano-Bicocca (Italy) as
subcontractors.
The goal of this presentation is to give an overview ofthe project activities and current status to the scientificcommunity in the field of remote sensing offluorescence. In this presentation, we will also describe
the entire L2A-to-L2D data processing chain, anddemonstrate the current accuracy of the implemented
algorithms through the latest performance assessment
results.

************************************************

10

Retrieval of the Sun-Induced Fluorescence in theframework of the FLEX mission

and far-red peaks, wavelengths of the maximum andspectrally integrated SIF). A first evaluation of theaccuracy obtained by the retrieval algorithm wasevaluated on radiative transfer simulations obtained bycoupling the SCOPE and MODTRAN5.
The retrieval algorithm was further adapted to process
the airborne imagery acquired collected by the highresolution imaging spectrometer HyPlant. A set offlight-lines collected during the recent FLEXSense
campaign carried out in 2018 were processed by thenovel algorithm and analyzed in comparison withground-based spectral measurements. For the first time
we were able to observe the full SIF spectrum ofdifferent crop fields (e.g., corn, alfalfa) and in general ofthe diverse land-cover types in the study areas, as wellto observe the temporal evolution along the summer
time period of the campaign (June-August). The
resolved fluorescence spectrum observed for thedifferent land cover types shows an extremely diverse
spectral behavior that it is function of a large number ofphysiological and chemical/physical variables thedifferent canopies. Finally, we assessed the accuracy of
the full fluorescence maps produced by a directcomparison with the SIF spectra obtained by theground-based spectrometers (FLOX instruments)
collected simultaneously to the airborne overpasses.

Cogliati S1, Celesti M1, Rascher U2, Rademske P2, Vicent

J3, Alonso L4, Sabater N4, Matot G3, Schuettemeyer D5,
Drusch M5, Colombo R1
1
University of Milano-Bicocca, 2Institute of Bio- andGeosciences, Forschungszentrum GmbH, 3Magellium,
4
University of Valencia, 5ESA-ESTECThe FLuORescence Imaging Spectrometer aboard of the
FLEX satellite is specifically designed to provide
radiance observations in high-spectral resolution (0.3nm) around the O2 bands, together with a broad
spectral coverage from 500 to 780 nm. This specificconfiguration was designed with the aim to: i) observe
the red and far-red fluorescence at the O2-B and O2-A
bands, or even the full SIF spectrum; ii) provide canopy
chemical/physical variables essential to interpret the
SIF (i.e., Leaf Area Index (LAI); Leaf Chlorophyll Content(LCC); Fraction Of Absorbed PAR (fAPAR), etc.) and the
PRI. This set of measurements will be further
complemented from the information provided by the
Ocean Land Color Imager (OLCI) and the Sea and Land
Surface Temperature Radiometer (SLSTR) instruments
aboard of the Copernicus Sentinel-3 (S-3) mission. The
S-3 will fly in tandem to FLEX providing all the key
information required to characterize the atmospherewith the accuracy required to retrieve SIF at the O2
bands and Solar Fraunhofer lines. This specific set-up
will offer a number of improved capabilities comparedwith the observations available by current satellites(e.g., OCO-2, TROPOMI etc.), such as the possibility tospectrally resolve the entire SIF spectrum in the 670780 nm range.

************************
From proximal sensing to satellite scale: Analyzing
and compensating atmospheric effects on oxygenfeatures for retrieving fluorescence.

Sabater N1, Alonso L1, Kolmonen P2, Vicent J3, Verrelst

J1, Middleton E4, Porcar-Castell J5, Atherton J5, Moreno
J1
1
Laboratory for Earth Observation (LEO). Image
Processing Laboratory (IPL). University of Valencia,
2
Atmospheric Radiation. Finnish Meteorological
Institute, 3Magellium, 4NASA Goddard Space Flight
Center, 5Optics of Photosynthesis Laboratory. Institutefor Atmospheric and Earth system research(INAR/Forest). University of Helsinki

This contribution aims to describe the overall conceptof the full SIF spectrum retrieval algorithm and theongoing development and testing activities on different
sensors. The algorithm is a revised approach of theoriginal version proposed in Cogliati et.al., 2015, where
the major improvement was the possibility to model/fit
the SIF spectrum with a very limited number ofparameters. The algorithm, initially developed onradiative transfer simulations, has been further
adapted to retrieve the fluorescence from ground andairborne spectrometers. In this contribution we will firstshow how the algorithm is going to be implemented
within the FLEX L2 processor under development in theframework of the ESA’s FLEX-L2RM project. Specifically,
the SIF retrieval algorithm is part in the so-called L2C
module of the FLEX L2R. It makes uses a set of input
variables produced by the L2A (spectral/radiometriccalibration) and L2B (atmospheric correction) modules
to retrieve SIF spectrum and a set of metrics (i.e. SIF
values at O2-A and O2-B, SIF at the maximum of the redIntheforthcoming
years,
satellite-derived
photosynthesis research will be advancing with theadvent of the ESA’s FLuorecence EXplorer (FLEX)
mission. Among other vegetation-related products,
FLEX aims to provide continuous measurements of SunInduced vegetation chlorophyll Fluorencence (SIF) from
650 nm to 780 nm at the high spatial resolution of 300
m. In this context, SIF estimations acquired at a lower
scale, either from systems mounted on towers,
Unmanned Aerial Vehicles (UAVs) or airborne
platforms, will become essential for FLEX – or any other11

fluorescence-related mission – preparatory activities
and validation campaigns.

Applications of fluorescence instress detection

Regardless of the vertical scale, proximal sensing orsatellite level, when retrieving SIF by especiallyresolving the strong oxygen (O₂) absorption features,
atmospheric effects must always be compensated. To
this end, this work provides an overview of the mostimportant aspects to be accounted for as part of theatmospheric correction process across contrastingvertical scales. In particular, we stress those key points
related to the atmospheric characterization, thealgebra involved, and the possible usage of the surface
apparent reflectance as a quality indicator.

Understanding the spectral changes associated to thephotoprotection (NPQ) mechanisms of vegetation:
Opportunities for FLEX-FLORIS LR (500-780 nm)
products

Thus, this work starts with a comprehensive analysis
about how atmospheric effects impact SIF estimations
on proximal sensing, thereby studying the influence of:(1) the sensor height above the vegetated canopy; (2)the SIF retrieval technique used, e.g., Fraunhofer Line
Discriminator (FLD) family or Spectral Fitting Methods(SFM); and (3) the instrument's spectral resolution. For
proximal–sensing scenarios, we demonstrate thatcompensating for atmospheric effects by simply
introducing the O₂ transmittance function into the FLD
or SFM formulations improves SIF estimations.
However, due to the algebra assumed thesecompensation strategies still derive some inaccuracies
within the absorption regions.

Van Wittenberghe S1, Alonso L1, Malenovský Z2, Porcar-

Castell A3, Moreno J1
University of Valencia, 2University of Tasmania,
3
University of HelsinkiWith ESA’s upcoming Fluorescence Explorer-Sentinel 3
tandem mission (FLEX-S3), not only the retrieval ofsolar-induced fluorescence (F) becomes a newopportunity for understanding plant functional
behaviour, also the photoprotection dynamics canpotentially be further understood. The Fluorescence
Imaging Spectrometer Low Resolution (FLORIS LR) on
board of FLEX will cover the 500-780 nm range with abandwidth between 0.1 nm and 2 nm, and a 1 nm
spectral resolution in the region of photoprotection
dynamics (500-740 nm). Photoprotection or controlled
non-photochemical energy quenching (NPQ) and F
emission are the two processes controlling the electrontransport to the photosynthesis reaction centres andare therefore indispensable for the development ofLevel-2D higher-level photosynthesis products for the
FLEX-S3 mission.
To safely balance out the energy supply to thephotosynthetic reaction centres, the photosynthesis
apparatus switches efficiently between a lightharvesting to a photoprotective mode in different
steps. These different controlled regulated heatdissipation mechanisms are activated inside the leaves
by various physical and biochemical triggers. The
spectral characterization of these NPQ mechanisms ischallenging due to several overlapping mechanisms
taking place on a diurnal scale. Besides the absorbancefeature related to the chemical xanthophyll conversion,
several additional overlapping NPQ absorbancefeatures are present in the vegetation spectrum. Strong
conformational pigment bed changes appear to be
responsible for a significant absorbance change in the
VIS-NIR range. The characterization of these spectral
absorbance features is a further step in the1

Looking towards a more rigorous atmosphericcompensation strategy, this work also assesses the pros
and cons of adapting a classic airborne atmosphericcorrection scheme to SIF proximal-sensing applications,e.g. addressed to systems mounted on towers or UAVs.
In addition, given the importance of O₂ absorption in
the SIF retrieval process, SIF retrieval dependency on
surface pressure (p) and air temperature (T) is also
evaluated, paying special attention to those
applications acquiring long temporal data series
subjected to abrupt changes in meteorologicalconditions.
Finally, since inaccuracies on the atmosphericcorrection process make SIF rapidly prone to errors, thiswork will close with a final discussion on the
exploitation of the surface apparent reflectance acrossdifferent vertical scales as a robust quality indicator.

************************

12understanding of dynamic plant behaviour regarding its
energy distribution, i.e. with a harvesting or adissipation fate. Current scientific developments in the
spectral characterization of the NPQ mechanisms arepresented, being, in combination with F retrieval, of ahighimportanceforassessingvegetation
photosynthesis from remote sensing.

photosynthetic efficiency (Fq’/Fm’) performance underelevated [CO2] measured in July 2018 by LIFT.
In winter wheat, active and passive fluorescence variedwith temperature changes in early spring and Fq’/Fm’
and SIF yield at 750 nm were positively correlated. In
soybean, passive fluorescence differed between twosoybean varieties when grown under elevated [CO2] inAugust. The effect of elevated [CO2] will be discussed
between and within species. In the latter the special
focus will be on the potential of using fluorescence asplant trait for phenotyping.

************************
Active and passive fluorescence measurements underelevated CO2 the field.

************************

Muller O , Junker L , Krause A , Pingle V , Jedmowski
1

1

1

1

C1, Acebron K1, Siegmann B1, Zendonadi N1, Soares J2,
Vasconcoles M2, Kraska T3, Rascher U1
1
Forschungszentrum Juelich, 2Universidade Católica
Portuguesa , 3University Bonn, Campus Klein-Altendorf
The increase of atmospheric CO2 concentration [CO2]has a direct effect on photosynthesis and plant
production. To study the effect of predicted [CO2]increase in the field Free Air CO2 Enrichment (FACE)
experiments have been developed. These FACE
experiments typically control [CO2] around 550 ppm
and have measured plant performance in diverse
ecosystems. In the agricultural ecosystems FACE
experiments have shown often a significant increase inyield whereas quality may decrease.
Yield and quality are key traits to select for new
varieties by breeders but they are breeding under lower[CO2] then when new varieties will be released undercurrent [CO2] increase predictions. To test (new) variety
performance the BREEDFACE was set up by
Forschungszentrum Juelich IBG-2 Plant Sciences inCampus Klein-Altendorf Germany. BREEDFACE allows
growth of crops combined with quantifying plant traits
with a large range of field phenotyping techniques.
In this presentation we will focus on active and passive
fluorescence measurements by two sensors, the Light
Induced Fluorescence Transient (LIFT) device and theFluorescence Box (FLOX) respectively. The LIFT device
retrieves fluorescence at 680 nm after activation byblue (470nm) light by a saturating sequence of flashlets
at high repetition rates. The FLOX enables passive
measurements of sun induced fluorescence (SIF) in theatmospheric oxygen absorption bands at 689 and
760nm. Both instruments were used to measure winterwheat in early cold spring and to study soybean
varieties grown under elevated and ambient [CO2] on a
hot summer day in 2018. Winter wheat varieties werechosen from an historic collection released from 1950
to 2013. Two to four soybean varieties were chosen out
of 18 varieties because of their contrasting

Calibration and validation ofsatellite data

Radiometric/spectral calibration and co-registration
correction algorithms for FLEX/Sentinel-3 Level-2
synergy

Vicent J1, Matot G1, Hillairet E1, Lemahieu C1, Ruiloba

R1, Drusch M2
Magellium, 2ESA/ESTEC, European Space Agency
In the context of ESA’s FLEX/Sentinel-3 mission Phase
C/D activities, an on-going 2-years project aims at
consolidating and validating the Level-2 data processing
chain. The retrieval of the L2 geophysical products fromthe FLEX/Sentinel-3 tandem mission, and in particular
the fluorescence retrieval, relies on measurementsfrom the FLORIS, OLCI and SLSTR instruments. The
Level-1b products of these instruments have to beharmonized with respect to their geolocation, spatial
resolution, and spectral information to ensure
consistent input data to the L2 retrieval algorithms.
Among the components of the L2 processing chain, theL2A module has a key role of harmonizing the
FLEX/Sentinel-3 Level-1b products, ensuring theconsistency between the various instruments for acorrect execution and accuracy of the next retrieval
modules. The L2A module which is divided in thefollowing steps:(1) Preliminary atmospheric characterization: extracts
meteorological data from existing datasets (S3 products
and ECMWF data) and derives a preliminary cloud maskfrom S3 L1B.
1

13

(2) Geometric co-registration: refines the geometricmodels of FLORIS images (from the FLORIS-HR and -LR
instruments), so that they could match together andwith Sentinel-3 acquisitions.
(3) Radiometric cross-calibration: calculates and applies
radiometric gain ratios by cross-calibration between
FLORIS and OLCI at different spectral bands,
harmonizing the radiometry of FLORIS, OLCI and SLSTR
instruments.
(4) Spectral-recalibration: the correct characterizationof the FLORIS ISRF is required in order to minimize error
propagation in the following L2 processing (particularlyin the atmospheric correction within the narrow O2bands). The algorithm, based on the use of solar and O2
absorption lines as reference, aims at reducing theuncertainties of the on-ground ISRF characterizationand of the in-flight distortions.
(5) Final ortho-rectification: re-projects the intercalibrated products into a common ground grid.

•Upgradingexisting
sites
with
new
instrumentation or establishing entirely newmonitoring sites to close thematic or geographic gaps;•
Implementing and maintaining a database forthe distribution of reference measurements (RMs) andthe corresponding Land Products (LPs).
GBOV service is primarily directed at the validation of
selected CGLS products (top-of-canopy reflectance,
surface albedo, leaf areas index, fraction of absorbed
PAR, fraction of vegetation cover, land surface
temperature and soil moisture), providing collections ofmultiple-year ground-based RMs as well as derived LPs.
The Earth Explorer - Fluorescence Explorer (FLEX)
mission will map vegetation fluorescence to quantify
photosynthetic activity. Among the standard products
to be generated by FLEX ground segment: LAI andFAPAR are among the validation products delivered by
GBOV service. This talk will present the GBOV
infrastructure and provide an overview of the services
and products offered as well as its potential for FLEX
validation.

This paper will give first an overview of the on-going
activities involving the generation of the Level-2asynergy data product. Secondly, we will focus on thealgorithms description for spectral re-calibration andradiometric cross-calibration of the FLORIS, OLCI and
SLSTR measurements. Finally, we will show validationand performance assessment results.

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Validation of Sentinel-2 cloud masking andclassification products – potential for Sentinel-3
validation?

************************

Main-Knorn M1, Pflug B1, Louis J2, Debaecker V2,

Mueller-Wilm U3, Boccia V4
DLR, 2Telespazio France - A Leonardo / Thales
Company, 3TPZV-D - Telespazio Vega Deutschland – A
Leonardo / Thales Company, 4ESAThe Copernicus Sentinel-2 mission is a constellation of
two polar orbiting, optical satellites Sentinel-2A and
Sentinel-2B delivering high spatial resolution data
products. This mission is dedicated to land monitoring,
emergency management and security. In particular, it
finds applications in land-cover change analysis,
retrieval of biophysical variables, monitoring of coastal
and inland waters as well as risk and disaster mapping.
1

Copernicus GBOV service: a support to FLEX products
validation

Lerebourg C1, Bai G1, Ronco E1, Bruniquel V1, Lamquin

N1, Henocq C1, Clerici M2, Gobron N2, Dash J3, Brown L3
ACRI-ST, 2JRC, 3University of Southampton
GBOV (Ground-Based Observations for Validation;
http://gbov.copernicus.acri.fr), part of Copernicus
Global Land Service (CGLS) is dedicated to the long term
validation of land products derived from satellite borne
sensors. Its prime objective is to facilitate the use ofground observations acquired from operational
monitoring networks and their comparison to Earth
Observation products providing ready to use up-scaled
product derived from consistent and documented
procedures. GBOV service as the following objectives:•
Collecting
multi-year
ground-based
observations of high relevance for the understanding ofland surface processes from existing global networks.
These ground-based observations are collected over aseries of selected sites operated by international
networks such as FluxNet, NEON, OZFlux, SurfRad,
TERN, USRCN, AERONET, ARM, BSRN …;

1

Since June 2017 the Copernicus Sentinel-2 mission is
fully operating while since March 2018, Level-2A
products are generated by the official Sentinel-2 groundsegment (PDGS) and are available on the Copernicus
Open Access Hub within 12 hours of sensing time. The
Level-2A processor for Sentinel-2 data – Sen2Cor –corrects monotemporal Level-1C Top-Of-Atmosphere
products from the effects of the atmosphere in order todeliver a Level-2A surface reflectance product. The
basic framework consists of two main modules: theScene Classification (SCL) and the Atmospheric
Correction (AC). The SCL algorithm allows to detect

14clouds, their shadows and snow, and to generate aclassification map with 11 classes. This map is usedinternally in Sen2Cor in the AC module to distinguishbetween cloudy, clear andwater pixels, but it does not perform a land coverclassification map in a strict sense.

Fluorescence (SIF) by means of a series ofspectrometers (FloxBox, JB, D) that were deployed in
the field in Italy, Germany, France and Spain. The Italianand German sites were focused on long-term
continuous SIF observations on crops and grasslands,
the French site was on a deciduous oak forest (Quercus
pubescens) and the Spanish site was installed over a
typical Dehesa land use made by a combination ofgrasslands and sparse holm oak trees. SIF dataacquisition at high temporal resolution started in
January 2018 and is still on going at all sites. This
presentation will summarize and discuss the different
datasets that are becoming available while otherpresentations will focus specifically on some key
findings of the AtmoFlex campaign.
This first campaign was then nested to a second ESAfunded project in the summer 2018, called FlexSense.
During such campaign during which several hundred
flight lines across five European core sites wererecorded with the high resolution airborne imaging
spectrometer HyPlant_3, which has improved optical
performance in comparison to the version flown theyears before. HyPlant_3 was mounted with an aligned
TASI sensor for thermal and a LIDAR sensor for 3-D
surface mapping on board a Cessna aircraft. HyPlant
images were acquired with different flight modes that
include low-altitude flights for high-resolution spatial
mapping and high altitude larger scale mapping in
synchrony with a constellation of Sentinel 3A and
Sentinel 3B to better understand the influence of
atmospheric properties onto fluorescence retrieval.
Thanks to the exceptional weather conditions in June
and July 2018, characterized by clear skies conditions,
we were able to record an unique data set of various
stressed and non-stressed vegetation types. A flexible
campaign planning enabled the use of this airborne
package at different sites, covering clear sky conditions
and facilitated the synchronous data acquisition withvarious ground activities and other airborne platforms
such as APEX and AVIRIS NG. This presentation, will
provide an overview on the available data by illustrating
the first maps of solar-induced fluorescence from
HyPlant_3. For the first time we could apply the spectral
fitting method (SFM), which will be the nominal
retrieval method for the FLEX satellite mission, for alarger set of HyPlant_3 images. This retrieval method
uses a carefully parameterized atmospheric correction
and a retrieval of both fluorescence peaks around theoxygen absorption bands. Maps of solar-induced
fluorescence are registered with images of land surface
temperature, structural vegetation properties, anddetailed ground-based measurements of the functional
status of various vegetation types. The dynamicchanges in the solar induced fluorescence andinformation that is contained in the two peak feature of

In the frame of the ESA Sentinel-2 Mission Performance
Center (MPC), the Level-2A validation strategy andoperational validation service is performed to ensure
the highest quality of provided Level-2A products. The
presentation gives an overview of the different steps of
the Sen2Cor Scene Classification algorithm and its
validation procedure. Validation results on someselected products as well as the current limitations of
the algorithm are presented. Finally, potential synergies
between Sentinel-2 and Sentinel-3 cloud screening
validation are addressed.

************************

Airborne and UAS campaigns

Collaborative Solar-induced fluorescencemeasurement campaigns – decsription of objectives,
ground / airborne measurements and preliminary
results

Rascher U1, Bendig J2, Burba M3, Burkart A4, Cogliati S5,Colombo R5, Damm A6, Drusch M3, Emin D1, Gamon J7,
Gauquelin T12, Godin S12, Hanus J8, Heinemann S1, Hueni
A6, Julitta T5, Junker L1, Krieger V1, Malenovsky Z2,
Martin M9, Matveeva M1, Migliavacca M9, Miglietta F10,
Muller O1, Näthe P1, Neininger B11, Paul-Limoges E6,
Rademske P1, Reiter I12, Sakowska K13, Siegmann B1, levan Suu A12, Wilke N1, Xueref-Remy I12, Schüttemeyer D3
1
Forschungszentrum Jülich, 2University of Tasmania,
3
European Space Agency - ESTEC, 4JB Hyperspectral,
5
University of Milano Biccoca, 6University of Zurich,
7
University of Nebrasca, 8Czech Globe, 9Max Planck
Institute of Biogeochemistry, 10CNR - IBIMET, 11MetAir
AG, 12CNR, 13University of Innsbruck
A number of multi-site campaigns were funded by ESA
in 2018 to gather new data on plant fluorescence under
different climates, seasons and land uses. A first project(AtmoFlex) was designed to acquire Solar Induces15fluorescence is discussed on the background of thefunctional acclimation of vegetation to diurnal,
seasonal and stress induced changes for which thesummer month in 2018 provided ideal conditions.

approach based on different image criteria to assess thequality of airborne SIF maps. The set of quality criteria(e.g. signal-to-noise ratio, correlation with vegetation
indices, plausibility checks, etc.) helps identifying andquantifying errors and artifacts in retrieved SIF maps.
In this contribution, we outline the defined set of
quality criteria and demonstrate their capability todetermine the quality of individual SIF maps derived
from HyPlant images acquired during the 2018
FLEXSense campaign. The application of the proposed
quality features proved to be a valuable tool forassessing the quality of SIF maps derived from HyPlant
airborne data. We suggest to apply this set of criteria in
addition to validation attempts that employ groundreference measurements. This allows providing
complementary information about the SIF retrieval
accuracy and the quality of entire SIF maps.

************************
Quantitative assessment of Sun-InducedFluorescence maps from HyPlant airborne images
using different quality criteria - Part I

Siegmann B1, Krieger V1, Matveeva M1, Rademske P1,Heid P1, Gruenhagen L1, Muller O1, Cogliati S2, Damm
A3, Rascher U1
1
Forschungszentrum Jülich, 2University of MilanoBicocca, 3University of Zurich
The ability to investigate the Earth’s environment will
be largely improved by hyperspectral satellite data. The
FLuorescence EXplorer (FLEX) will be the first
hyperspectral mission designed to monitor thephotosynthetic activity of the terrestrial vegetation
layer by using a completely novel technique measuring
the sun-induced chlorophyll fluorescence (SIF) signalthat originates from the core of the photosynthetic
machinery. In preparation of the upcoming FLEX
satellite mission that will be launched in 2022, a large
field campaign, namely FLEXSense, was conducted insummer 2018 including representative study sites atseveral locations in middle and south Europe as well asNorth America.
During the various field activities, airborne data wereacquired with the hyperspectral airborne imager
HyPlant that consists of two sensor heads. The DUAL
module is a line-imaging push-broom sensor providing
contiguous spectral information from 370 to 2500 nm.
The FLUO module measures radiance in high spectral
resolution (0.25 nm) in the spectral region of the twooxygen absorption bands covering a range from 670 to
780 nm and facilitates a reliable retrieval of thechlorophyll fluorescence signal. Currently, two different
algorithms are routinely used to retrieve red (SIF680)
and far-red SIF (SIF760) from HyPlant data. Bothmethods exploit the oxygen absorption bands for the
retrieval. While the improved Fraunhofer Line Depth(iFLD) approach employs a semi-empirical atmosphericcorrection (i.e. using bare soils), the Spectral Fitting
method (SFM) is coupled with a physically-based
atmospheric correction (MODTRAN5 code).
A common method of testing the reliability of remotelysensed SIF (in this study airborne maps) is thecomparison with “ground truth” data. In many cases,
however, ground measurements of SIF are not available
or are too labor-intensive to be measured at regional
level. For this reason, we developed an alternative

Since the quality assessment using the different criteria
is very extensive, only a part will be covered in this talkwhile the remaining criteria and their application will bepresented in form of a poster (additional contribution:
V. Krieger; B. Siegmann; M. Matveeva; P. Rademske; P.
Heid; L. Grünhagen; O. Muller; S. Cogliati; A. Damm andU. Rascher – Quantitative assessment of Sun-InducedFluorescence maps from HyPlant airborne images using
different quality criteria - Part II)************************
UAS-based Chlorophyll Fluorescence Measurementsof Barley Canopies – Results from FLEXSense 2018

Bendig J1, Malenovský Z1, Siegmann B2, Rademske P2,

Krause A2, Gruenhagen L2, Koenig S2, Prüm M3,
Gautam D1,4, Rascher U2, Lucieer A1
1
University Of Tasmania, 2Research Centre Juelich,
3
Rhine-Waal University of Applied Sciences, 4Universityof Adelaide
This study presents the first multiscale SIF dataset,
where field and airborne observations are accompanied
by unmanned airborne system (UAS) measurements. A
dataset of diurnal UAS-spectroscopy for retrieval ofsolar-induced chlorophyll fluorescence (SIF) was
acquired in June 2018 during the FLuorescence EXplorer(FLEX) calibration/validation campaign (FLEXSense
2018). While preparation of the FLEX mission is inprogress, airborne, drone and ground data collected
simultaneously with Sentinel 3A and Sentinel 3B are
expected to contribute to a better understanding of thefluorescence signal and retrieval techniques acrossdifferent spatial mapping scales. The UAS-based systempresented here, called AirSIF, is built on a dual opticalpathway and a high resolution spectroradiometer
installed on a low-altitude multi-rotor remotely piloted

16

Waters - Research and Management, Eawag, Swiss
Federal Institute of Aquatic Science and Technology,
8600 Dübendorf, Switzerland, 3JB Hyperspectral
Devices UG, Am Botanischen Garten 33, 40225,
Düsseldorf, Germany, 4Remote Sensing ofEnvironmental Dynamics Laboratory, Department ofEarth and Environmental Sciences (DISAT), Universityof Milano-Bicocca, Piazza della Scienza 1, Milano
20126, Italy, 5Department of Biogeochemical
Integration, Max Planck Institute for Biogeochemistry,Hans-Knoell-Str. 10, 07745 Jena, Germany, 6Institute of
Biometeorology, National Research Council (IBIMETCNR), Via Caproni 8, Firenze 50145, Italy, 7European
Space Agency (ESA-ESTEC), Keplerlaan 1, 2201 AZ
Noordwijk, The Netherlands
The upcoming satellite mission Fluorescence Explorer(FLEX), currently under development by the European
Space Agency, will provide after its launch in 2022
global information of fluorescence and photosynthetic
activity. Coherence of fluorescence observations fromin-situ, airborne, and satellite platforms for different
ecosystems is key to retrieve robust novel plant
physiological information form this new data source.
The complexity and information content of observed
fluorescence signals, however, changes withobservational scale and challenges comparability ofsuch measurements. In situ measurements, forexample, are representative for small surface areas andare collected in close distance to the surface with hightemporal resolution (minute based). Satellite
observations are able to collect fluorescence emissionsof large areas but lack temporal resolution (monthly
based).

platform. The spectroradiometer acquisitions aresynchronised with readings of an on-board Inertial
Measurement Unit (IMU)/ Global Navigation Satellite
System (GNSS) system, which enables to reconstructgeometrically and spatially explicit footprints of thespectroradiometer SIF measurements during a flight.
The study was conducted at a plant breeding and fieldtrial agricultural station in Western Germany, near
Bonn. 11 summer barley experimental plots of a size of3 x 6 m were monitored diurnally within four UAS flights
carried out between 12:00 and 17:00 local summer
time. A hovering style of UAS data acquisition (named“stop and go”) allowed us to assess the stability of SIF
values retrieved from footprints over the experimental
plots (n = 119). Each plot was set as a waypoint in the
UAS flight path. The UAS was flown at 8 m above groundlevel at 1.5 m/s ground speed. Upon reaching the
waypoint, the UAS hovered above a plot for 15 seconds
while the spectroradiometer acquired data
continuously. Between one and six measurements weretaken of each plot per flight. The resulting
spectroradiometer footprints varied from 0.5 to 2.5 m²
in size, depending on UAS actual position drifts during
hovering. The SIF values measured have a mean of 0.83
mW.m-2.nm-1.sr-1, a median of 0.84 mW.m-2.nm-1.sr1, and standard deviation of 0.59 mW.m-2.nm-1.sr-1.
The values are being analysed and will be comparedagainst ground-based FLOX box measurements,
collected for some experimental plots just before andafter UAS acquisitions, and SIF retrieved from 1 mground resolution airborne Hyplant_3 image data,acquired almost simultaneously.

************************

We present the design and function of the centralised
data base system FluoSPECCHIO, which is an extensionof the spectral information system SPECCHIO(www.specchio.ch). The development of this system
was triggered by the need for a coherent strategy toobtain cross scale (both temporal and spatial)
fluorescence measurements stemming from a growing
network of in-situ measurements distributed across adiversity of ecosystems and an increasing number ofairborne and satellite platforms. The databasefacilitates ingesting point observations by the
Fluorescence Box (FLOX) manufactured by JB
Hyperspectral Devices, currently establishing astandard for a fast growing in-situ network ofmeasurement sites worldwide.

In situ measurement offluorescence I

FluoSPECCHIO: A spectral data base system tofacilitate a validation network for the upcoming
Fluorescence Explorer (FLEX) mission
Damm A1,2, Burkart A3, Celesti M4, Cogliati S4, Hueni A1,
Julitta T3, Migliavacca M5, Miglietta F6, Schuettemeyer
D7, Trim S1, Colombo R4
1
Remote Sensing Laboratories, Department ofGeography, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland, 2Department of Surface

We demonstrate the functioning of the data basesystem including its capability to autonomously readand process FLOX data. We outline possibilities for how
FluoSPECCHIO can facilitate the development of a17

validation network for the upcoming FLEX Sentinel-3
mission.

canopy level in response to rising temperatures during
spring.

************************************************
Filtering Fluorescence Time Series Acquired with the
FloX Monitoring Field Spectrometer for theInvestigation of Vegetation Dynamic Seasonal Trends
over Grassland

Näthe P1,2,7, Burkart A1, Julitta T1, Junker L2, Knaps A3,

Bohn B4, Pospichal B6, Jonard F5, Lud D7, Rascher U2
JB Hyperspectral Devices, 2IBG-2: Plant Sciences,
Institute of Bio- and Geoscience, Forschungszentrum
Jülich, 3S-UM: Meteorology, Department for Safety andRadiation Protection, Forschungszentrum Jülich, 4IEK-8:
Troposphere, Institute for Energy- and Climate
Research, Forschungszentrum Jülich, 5IBG-3:
Agrosphere, Institute of Bio- and Geoscience,
Forschungszentrum Jülich, 6IGMK, Institute ofGeophysics and Meteorology, University of Cologne,
7
Faculty of Communication and Environment, RhineWaal University of Applied Sciences
The process of photosynthesis feeds almost all livingorganisms on the planet, plays an important role in the
global carbon cycle and directly impacts the climate on
earth. Remote sensing of sun induced chlorophyll
fluorescence (SIF) is applied for non-invasive
monitoring of photosynthesis in terrestrial vegetation
on various scales. However, the direct understanding of
SIF as a proxy for photosynthesis is a field of ongoing
research. Tower-based SIF retrieval by field
spectrometers for autonomous long-term observationof vegetation contributes to gain further insight into
ecosystem-specificseasonal
dynamicsofphotosynthesis activity.
In this work we investigate quality criteria for long-term
SIF measurements collected with FloX monitoring field
spectrometers (JB Hyperspectral Devices, Düsseldorf,
Germany) based on instrument characteristics,
calibration, performance parameters and setup. Basedon these derived quality criteria, we propose a filtering
protocol for SIF data retrieved with the FloX monitoring
field spectrometers. Furthermore, the impact ofchanging diffuse light ratio on seasonal trends of SIF
Yield is investigated and shown to be neglectable withintime series. Seasonal trends of midday-mean, filtered,apparent SIF Yield are examined over grassland inGermany during spring 2018 based on FloX data. We
relate apparent SIF Yield with the help of vegetation
indices (VI) to phenological and physiological changes at
canopy level. This research indicates that filtered,apparent SIF Yield monitors in combination with VI
phenological and physiological changes of grassland at118

the use of FLORIS data alone improves greatly the
results (R²: 0.97; relative RMSE: 8.9%). Further, merging
the OLCI and the FLORIS spectra does not significantly
improve the results (R²: 0.96; relative RMSE: 8.5%).
Regarding LAI retrieval, the improvement of the model
performances by using only FLORIS spectra (R²: 0.82;
relative RMSE: 30.7%) rather than only OLCI spectra (R²:0.81; relative RMSE: 32.0%) is less obvious but thesynergy of both datasets is more advantageous (R²:0.87; relative RMSE: 27.0%). The models for the
retrieval of fAPAR, regardless of on which dataset they
are based, are performing particularly well (average R2:
0.96; average relative RMSE: 7.3%). APAR on the other
hand, will be predicted from the fAPAR model bymultiplying the fAPAR estimations with PAR, which will
be a L2B-level product. At last, the retrieval model for
FVC, which is neither an input nor an output variable of
SCOPE, is based on field data and yields rather good
performances (R²: 0.92; relative RMSE: 18.3%). These
results show that the retrieval models for the
traditional biophysical variables are already quite
robust in their first version. These models have been
integrated in the L2D module of the FLEX Level 2
project, which streamlines the processing of OLCI andFLORIS Level 1 data until florescence retrieval and theretrieval of vegetation variables. Finally, the OLCI
models have been successfully tested on real Sentinel3 images.

Retrieval of biophysicalparameters from FLEX and
Sentinel-3 data

Status on the retrieval models for the traditional
biophysical variables (LAI, Cab, fAPAR, FVC and APAR)

De Grave C1, Verrelst J1, Morcillo Pallarés P1, Rivera-

Caicedo J2, Moreno J1Laboratory for Earth Observation, University Of
Valencia, 2Secretary of Research and Postgraduate,
CONACYT-UAN
The biophysical parameters will be retrieved by use of a
hybrid method combining a non-parametric Machine
Learning Regression Algorithm (MLRA) and a vegetation
Radiative Transfer Model (RTM). OLCI (imaging
spectrometer on Sentinel-3) and FLORIS (hyperspectral
imager on FLEX) Top-Of-Canopy (TOC) reflectances are
simulated with the RTM SCOPE and subsequently
injected with a specific amount of Gaussian white noiseto account for the natural variability existing within the
300m-pixels of the FLEX-Sent-3 tandem mission. The
resulting database of vegetation properties andcorresponding TOC reflectances, covering a wide range
of geometrical configurations and canopy realisations,is then used to train the MLRA Gaussian Process
Regression (GPR) and generate the retrieval models.
These models are based on either OLCI spectra alone,on FLORIS spectra alone, or on the combined spectra ofboth instruments. Several steps in the retrieval
procedure can be optimized in order to provide
enhanced model predictions: the range of the input
variables of SCOPE, the size of the training database andthe amount of noise. At present, the models are
optimized using SCOPE simulated reflectance spectra.
In a second step, when close-to-real atmosphericallycorrected images coming from the FLEX End-to-End
Mission Performance Simulator will be available, amore accurate noise estimation will enable further
model optimization. The first version of the retrieval
models for Leaf Area Index (LAI), Leaf ChlorophyllContent(Cab)andfractionofAbsorbed
Photosynthetically Active Radiation (fAPAR) werevalidated on reference images which are simulated withan in-house developed Automated Scene Generator
Module (A-SGM) scientific toolbox. For Cab retrieval,the OLCI spectral data alone give reasonable model
performances despite the limited number of bands
involved (R²: 0.90; relative RMSE: 14.0%). Conversely,1************************

19

Global sensitivity analysis of coupled SCOPE-6S
model.

The project has received funding from the European
Union’s Horizon 2020 research and innovation
programme under the Marie Sklodowska-Curie grant
agreement No 721995.
References1.
Van der Tol, C.; Verhoef, W.; Timmermans, J.;
Verhoef, A.; Su, Z. An integrated model of soil-canopy
spectral radiances, photosynthesis, fluorescence,
temperature and energy balance. Biogeosciences 2009,
6, 3109–3129, doi:10.5194/bg-6-3109-2009.
2.
Vermote, E. F.; Tanre, D.; Deuze, J. L.; Herman,
M.; Morcette, J.-J. Second Simulation of the Satellite
Signal in the Solar Spectrum, 6S: an overview. IEEE
Trans. Geosci. Remote Sens. 1997, 35, 675–686,
doi:10.1109/36.581987.
3.
Wilson, R. T. Py6S: A Python interface to the 6S
radiative transfer model. Comput. Geosci. 2013, 51,
166–171, doi:10.1016/j.cageo.2012.08.002.

Prikaziuk E1, Van der Tol C1Faculty of Geo-Information Science and Earth
Observation (ITC), University Of Twente
We quantified the relative importance of different
Sentinel-3 bands for retrieval of plant traits andatmospheric composition parameters by coupling aland surface (SCOPE [1]) and an atmospheric radiativetransfer model (S6 [2,3]). For this purpose, we
simulated top of atmosphere (TOA) radiance of the two
instruments on-board of Sentinel-3 (Ocean and Land
Colour Instrument, OLCI and Sea and Land Surface
Temperature Radiometer, SLSTR), and carried out asensitivity analysis of these radiances to vegetation, soil
and atmospheric parameters. The SCOPE model
parameters included in the sensitivity analysis were leaf
traits(chlorophylls,
Cab;carotenoids,Cca;anthocyanins, Cant; water thickness, Cw; dry matter
content, Cdm; senescent material, Cs; leaf mesophyll
structure parameter, N), canopy traits (leaf area index,
LAI; leaf inclination distribution functions parameters,
LIDFa, LIDFb) and soil traits (brightness, B; soil moisture
content, SMC). Top of canopy reflectance simulatedwith SCOPE was propagated through the atmosphere to
produce TOA radiance. The atmospheric propagation
was carried out with 6S using a “Continental” aerosol
distribution profile scaled to provided aerosol optical
thickness values (AOT). Water and ozone values wereused to scale “us standard 62” atmospheric profile.
Three parameters of 6S model (AOT, water and ozone)
were used in the sensitivity analysis. TOA radiancevalues were integrated with the sensor response
functions of OLCI and SLSTR. The global sensitivity
analysis was done against 15 parameters with Saltelli
sampling and Sobol method.
The results demonstrated that LAI and soil brightness
had high impact on all the bands of both OLCI and SLSTR
instruments. As expected, chlorophyll content
significantly influenced bands Oa06-11 (561-709 nm)
and S1-2 (554, 659 nm) and water content (both leaf
and atmospheric) Oa20-21 (941, 1025 nm) and S4-6
(1375, 1613, 2256 nm). Bands beyond 750 nm weresensitive to dry matter content. The rest of theparameters showed low impact on TOA radiance withtotal sensitivity index close to 0.05, whereas N
parameter did not demonstrate its importance at all.
The next step in the analysis will be the inclusion of the
SLSTR bands in the thermal domain S7-9 (3.7, 10.8, 12.0um). The results will be used for the development of a
retrieval algorithm of land surface properties from
Sentinel-3.
1************************

20

other hand, both npq mutants showed a decreased
SIFyield at the end of the day compared to the firstmorning reading while PSII operating efficiency(Fq’/Fm’) were also reduced compared to WT
suggesting damaged PSII activity due to reduced
photoprotective capacity. The decline in SIFyieldobserved in npq mutants during summer is more
pronounced in all plant types diurnally measured during
winter. This decline is attributed to the development ofphotoinhibition, as confirmed by the decline of Fq’/Fm’
and reduced recovery of maximum PSII efficiency(Fv/Fm). Cluster analysis of spectral reflectance data (in400-750 nm range) obtained in the summer correctly
separated npq1 from both WT and npq4. This led to theconclusion that spectral reflectance can resolve
zeaxanthin accumulation, which is correlated tozeaxanthin-related NPQ in some conditions, but not
PsbS-related NPQ. Closer inspection of spectralreflectance data revealed changes in reflectancepeaking at 520 nm which can be attributed to thexanthophyll cycle, and in addition, other spectralfeatures which cannot be attributable to changes in thexanthophyll-cycle pigments but instead ascribed totemporal change during the day. The latter included
peaks at 553 nm, 630 nm and 700 nm which wereconsistently increasing towards the end of the day in allplants. This observation is important in accounting NPQ
contribution in dynamic changes of SIF signal andspectral reflectance. Additionally, the results showed
may provide additional insights for the temporal
sampling of FLEX mission to observe fluorescence ofterrestrial vegetation.

Modelling approaches acrossspatial and temporal scales I

Investigating diurnal change in spectral reflectanceand solar-induced fluorescence to understand non
photochemical activity (NPQ) of Arabidopsis npq
mutants

Acebron K1, Matsubara S1, Jedmowski C1, Emin D1,

Bennertz S1, Muller O1, Rascher U1
1
IBG-2 (Plant Science), Forschungszentrum Jülich
Photochemical and non-photochemical energy
dissipation in plants co-occur simultaneously to balance
the use of absorbed light energy between
photosynthesis and photoprotection. This energybalance is even more important during high light andfluctuating light conditions. While the photochemical
and non-photochemical contributions to fluorescencequenching can be resolved using active methods ofmeasuring chlorophyll fluorescence, passively retrieved
sun-induced fluorescence (SIF) cannot discriminate
these energy traps. If we are to quantify plant
productivity using SIF, as envisioned in Fluorescence
Explorer (FLEX) mission, it is important to understandthe changes in spectral reflectance and SIF that can be
attributed to photochemical and non-photochemical
activity. In this study, we investigated the effect of
reduced NPQ capacity on SIFyield and spectralreflectance by measuring diurnally Arabidopsis thaliana
mutants, one being deficient in zeaxanthin (npq1) and
one lacking PsbS protein (npq4), the two components
which are essential for NPQ in land plants. We observed
a similar increase in SIFyield for both npq mutants
compared to wildtype (WT) despite a difference infunctional NPQ mechanism. Simultaneous active andpassive fluorescence measurements were conducted
diurnally to understand the photochemical and nonphotochemical contribution in SIFyield. We extended
this investigation by comparing the diurnal
measurements in summer and winter to examine theeffect of photoinhibition (qI) caused by low
temperature. In summer, we observed higher SIFyieldfrom morning to midday in both npq mutants ascompared to the WT. At the end of the day, SIFyield of
WT recovered from midday depression and the values
were higher than the first measurement done in themorning, indicating a functional photoprotective
mechanism for Photosystem II (PSII) activity. On the************************

Downscaling of the solar-induced chlorophyll
fluorescence from canopy level to leaf/photosystem
level

Liu X1,2, Guanter L2, Liu L1

Key Laboratory of Digital Earth Science, Institute ofRemote Sensing and Digital Earth, Chinese Academy of
Sciences, 2Helmholtz Center Potsdam, GFZ German
Research Center for Geosciences, Remote Sensing
SectionSolar-induced chlorophyll fluorescence (SIF), an
electromagnetic signal that can potentially indicate
vegetation photosynthetic activity, can be retrieved
fromground-based,
airborneandsatellite
measurements. However, due to the scattering and reabsorption effects inside the leaves and canopy, SIF
measured at the canopy level is only a small part of thetotal SIF emission at the photosystem level. Therefore,a downscaling mechanism of SIF from the canopy levelto the photosystem level is important for better
understanding the relationship between SIF and the121

vegetation gross primary production (GPP). Using asimple parameterization model based on the spectral
invariant theory, we found that the probability for SIF
photons to escape from the canopy was related to theanisotropic spectral reflectance, canopy interception of
the upward solar radiation, and leaf absorption. An
empirical approach based on machine learning wasapplied to downscale SIF constrained by the red, rededge and far-red anisotropic reflectance, based on a
training dataset generated by the SCOPE model,
ground-based, airborne, and satellite observations
were used to test the performance of the SIF
downscaling approach. Results show that retrieved
total SIF at the photosystem level matches well withsimulated reference data, and the relationship between
SIF and photosynthetically active radiation absorbed bychlorophyll is obviously improved by SIF downscaling.
These results in combination with other evaluation
criteria suggests the downscaling of canopy SIF as anefficient strategy to normalize species dependent
effects of canopy structure and varying solar-viewgeometries.

that are represented by leaves, branches and trunks
built out of triangular facets. Plant 3D representationsof different structural and optical attributes are
distributed within a 3D scene to produce naturalvariability of vegetation canopies in terms ofbiochemistry, leaf area index, leaf angular distribution,
clumping of canopy elements, and canopy closure. This
ensures a rigorous simulation of photon interactions,i.e. reflected sunlight and emitted fluorescence, within
the objects a given 3D scene. Coupling with the
FLUSPECT leaf radiative transfer model enabled DART
to simulate top-of-canopy and within-atmosphere
solar-induced chlorophyll fluorescence (SIF, 640-850nm), accounting also for scattering and reabsorption by
non-photosynthetically active components such aswood.
Recent advances in high-performance computer
systems and exploitation of high-density terrestrial
laser scanning (TLS) data allowed for modelling of more
realistic 3D virtual forest scenes. Taking advantage ofthese resources, we have created 3D computer
representations of architecturally highly complex
coniferous Norway spruce (Picea abies) and broadleaf
Australian White peppermint (Eucalyptus pulchella),retaining realistic and biologically correct foliage andwood distributions. To evaluate the effects of canopy
structures on SIF emissions and reabsorption, we
simulated different DART scenarios where only one
component of the 3D tree representations was changed
at the time. Results of all scenarios were crosscompared to identify the key drivers modulating the
top-of-canopy SIF peaks at 687 and 740 nm. We
investigated the potential influence of wood elements(trunks and branches with various barks), the impact offoliage density and canopy clumping under a constantforest stand LAI, changes in SIF triggered by different
optical properties of spruce shoot twigs, and otheraspects of the forested scenes. DART results indicate asignificant sensitivity of the forest canopy SIF to woody
components. Presence of trunks and branches in P.
abies stands decreased canopy SIF by 15% and 32% at
687 and 740 nm, respectively. A decrease in the canopy
closure, i.e. clumping trees while keeping the total
stand LAI of 2, lowered SIF of the E. pulchella stand at
740 nm by 35%. The presence of woody components
decreased SIF at 740 nm by 24% in dense and 14% insparse Eucalyptus forest. 17% and 10% of these declines
were due to shadowing from woody structures thatlowered the fraction of photosynthetically active
radiation absorbed by leaves (fAPAR), while 7% and 4%of SIF emissions were absorbed by bark. By contrast,
replacement of the spruce needle-twig bark opticalproperties by the reflectance of green needles
increased the red and the far-red canopy SIF values by
12% and 24%, respectively. These sensitivity analyses************************
Sensitivity analyses of forest canopy chlorophyll
fluorescence using TLS-reconstructed stands in DARTMalenovský Z1, Janoutová R2, Gastellu-Etchegorry J3,

Yin T4,5, Lauret N3, Chavanon E3, Guilleux J3, Homolová
L2, Morton D5, Cook B5
1
University of Tasmania, 2Global Change ResearchInstitute of the Czech Academy of Sciences, 3Centred'Etudes Spatiales de la Biosphère, 4University of
Maryland, 5NASA Goddard Space Flight Centre
The signal of solar-induced fluorescence (SIF) estimatedwith various satellite sensors has improved modelling ofvegetation gross primary production at the global scale.
Yet, remotely sensed SIF retrieved for forested biomes,
such as tropical and boreal forests, were reported to besystematically lower in comparison to spatiallyhomogeneous vegetations types, e.g. agricultural crops.
Evidently, interpretation of forest SIF observations
requires further understanding of the SIF interactions
within structurally complex and heterogeneous forest
canopies. With this motivation in mind, the threedimensional (3D) discrete anisotropic radiative transfer(DART) model was enabled to simulate and upscale thechlorophyll fluorescence emissions from single leaves
up to complex plant (forest) canopies. DART calculates
the radiative budget and simulated air- and spaceborne images of various Earth surface elements fromvisible to thermal infrared wavelengths at various
spatial and spectral resolutions. It uses virtual 3D plants

22

demonstrated that DART simulations of the detailed
TLS-reconstructed forest stands can provide uniqueinsights regarding the sensitivity of top-of-canopy SIF tovarious forest structural and spectral properties, which
would be difficult to unambiguously identify via
experimental measurements.

The Inversion Lab, 2University of Reading, 3LudwigMaximilian University, 4University College London, 5ESA
The potential synergies offered by the complementary
use of FLEX, BIOMASS, S1, S2, S3, SMOS, TerraSAR-X andother non-European missions (e.g., GEDI, NISAR) will
open a unique opportunity to address the mainknowledge gaps in terrestrial carbon science. Suchcomplementary use could happen, for example, at thelevel of bio- and geophysical variables that are retrieval
products from individual missions through joint
assimilation into a comprehensive process model of theterrestrial carbon cycle, with suitable observation
operators for each of these products.
1************************

Modelling approaches acrossspatial and temporal scales II

Alternatively the synergy can already be exploited in the
retrieval process through a multi-mission retrieval, in
which a set of bio- and geophysical variables is retrieved
such that (with suitable observation operators in theform of radiative transfer models) it simultaneously
provides the best-possible match to observations frommultiple missions at the sensor level. Such a multimission retrieval has the potential to avoid theambiguities that single mission retrievals typically face(too many unknowns to be constrained by a singe
mission) and to improve the temporal and spatial
coverage of the retrieval products.

Assimilating satellite SIF into a process-based
terrestrial biosphere model: BETHY-SCOPE
Norton A1, Rayner P1, Koffi E2, Scholze M3, Silver J1,
Wang Y4
1
University Of Melbourne, 2European Commission Joint
Research Centre, 3Department of Physical Geography
and Ecosystem Science, Lund University, 4CSIRO
Satellite measurements of solar-induced chlorophyll
fluorescence (SIF) offer an unprecedented insight into
photosynthesis across spatial scales. The developmentof frameworks that utilise SIF to improve models of theterrestrial biosphere is critical to maximising the benefitof these measurements. Here we will present a data
assimilation framework for SIF using the process-basedmodel BETHY-SCOPE. Results from the assimilation of
SIF from the Orbiting Carbon Observatory 2 will bepresented. These SIF measurements are utilised toestimate biophysical parameters and gross primary
production (GPP). With this, strong uncertainty
reductions are found for biophysical parameters and
GPP. Additionally, the assimilation results in large shifts
in the global distribution of GPP. We will highlight thestrengths and weaknesses of this framework and show
how this may be expanded to include other satellite SIF
products such as FLEX.

The ESA-funded S3 - SENTINEL SYNERGY STUDY has
developed such a synergistic multi-mission retrieval
system. The system combines observations from an
optical sensor (Sentinel 2) with observations from anactive microwave system (Sentinel 1) in a weak
constraint variational data assimilation approach. The
dynamical model that is needed to close the gap
between the acquisitions of the satellites formalises our
expectation of the temporal evolution of the land
surface state. It is deliberately simple and assigned a
low weight such that the retrieval algorithm has much
freedom to deviate from this model. This choice
ensures a high impact of the Sentinel observations on
our retrieval products. Our state space contains LAI,
vegetation height, and soil moisture. From these direct
retrieval products we derive further retrieval products
such as FAPAR and phenology. The system uses two
physically consistent radiative transfer models, thesemidiscrete model for the optical domain and thesingle scattering radiative transfer (SSRT) model for the
microwave domain. There are two sets of priorinformation: The first one is a generic time and space
independent prior and the second one is derived fromsimulations with the Joint UK Land Environment
Simulator (JULES). The algorithm provides time varying
per-pixel uncertainty estimates for each variable
including the uncertainty correlation between
variables.

************************

Towards exploiting the carbon constellation ofsatellite missions: Using a variational data
assimilation approach for a synergistic multimission retrieval of bio- and geophysical variablesfrom Sentinel-1 and Sentinel-2 data.

Kaminski T1, Voßbeck M1, Quaife T2, Pinnington E2,
Marzahn P3, Timmermans J4, Rommen B5, Isola C523

Here I use a two stream model for fluorescence that is
capable of translating between leaf scale models of SIF
and the canopy leaving radiance taking into account alllevels of photon scattering and use it to forward model
SIF observations from JULES (the Joint UK Land
Environment Simulator) which is the land surface modelof the new UK Earth System Model (UKESM). Other suchfluorescence models have been developed previously
but the model described here is physically consistent
with the Sellers’ two stream radiative transfer scheme
which is widely used in modern land surface models.
Consequently any model that already employs the
Sellers’s scheme can use the new model without
requiring modification.

In the study, the system is applied over an agriculturallandscape. Results are validated against fieldmeasurements over the Munich-North-Isar site,Germany. The comparison with the field data
demonstrates how the retrieval of bio- and geophysicalvariables benefits from the synergistic approach. It will
be highlighted that the retrieval of soil moisture greatly
benefits from the simultaneous retrieval with LAI. On
the other hand, the high frequency of Sentinel 1
acquisitions improves the retrieval of an LAI timeseries. Through analysis of a series of satellite
unavailability scenarios we quantify the contribution ofindividual
satellites
andspecificband
combinations/polarisations on the uncertainty in the
retrieval products and on temporal consistency.
The retrieval system is designed in a modular andflexible way in order to facilitate integration ofobservation operators for further missions.

The JULES-SIF model is run at a number of sites where
measurements are available. Results show that it ispossible to reproduce the observed SIF signal, but that
understanding the magnitude of non-photochemical
quenching is key to making correct predictions.

************************************************

Forward modelling of Solar Induced Fluorescencefrom the JULES land surface model

Fluorescence for aquatic research
I-II

Quaife T1,2, Calder-Potts W1,2, McGuire P2

National Centre For Earth Observation, 2Departmentof Meteorology
Solar induced fluorescence (SIF) is becoming widelyused as a proxy for gross primary productivity (GPP), in
particular with the advent of its measurement by Earth
Observation satellites such as OCO and GOSAT. The
upcoming launch of FLEX offers exciting newopportunities to understand these processes at a muchfiner spatial resolution.
1

FLEX2018 cruise: preliminary results for the biooptical characterization of the investigated coastal
area (Tyrrhenian Sea)

Di Cicco A1, Colella S1, Bracaglia M1,2, Brando V1, Dionisi
D1, Falcini F1, Leonelli F1,3, Sammartino M1, Volpe G1,
Angelini F4, Artuso F4, Cataldi D4, Colao F4, Fiorani L4,
Lai A4, Nuvoli M4, Cesana I5,6, Santoleri R7
1
Italian National Research Council – Institute of Marine
Sciences (CNR – ISMAR), 2University of Naples
Parthenope, 3Sapienza University of Rome Department of Mathematics, 4Italian National Agency
for New Technologies, Energy and Sustainable
Economic Development (ENEA), 5University of Milano Bicocca, 6Italian National Research Council – Institutefor Electromagnetic Sensing of the Environment (CNR –IREA), 7Italian National Research Council – Institute ofMarine Sciences (CNR – ISMAR)
In the framework of the ESA “FLEXSense Campaign
2018” and Copernicus Marine Environmental
Monitoring Service (CMEMS) project, the Global Ocean
Satellite monitoring and marine ecosystem group (GOS)A major attraction of SIF is that it is independent of theassumptions embedded in light use efficiency based
GPP products derived from satellite missions such as
MODIS. The assumptions in such products are likely notcompatible with any given land surface model andhence comparing the two is problematic. On the other
hand to compare land surface model predictions of GPP
to satellite based SIF data requires either (a) translationof SIF into estimates of GPP, or (b) direct predictions of
SIF from the land surface model itself. The former
typically relies on empirical relationships, whereas thelatter can make direct use of our physiologicalunderstanding of the link between photosynthesis andfluorescence at the leaf scale and is therefore
preferable.

24

of the Italian National Research Council (CNR) organized
the oceanographic cruise “FLEX2018” in coastal watersof the Tyrrhenian Sea, providing a ground station forseveral bio-optical instruments onboard the CNR
research vessel “Dallaporta”.
The GOS sampling activities were conducted in timing
synergy with space (Sentinel 3A and Sentinel 3B) andairborne observations, with the intent to contribute to
the calibration/validation activities for existing andfuture mission developments.
Here, we present the preliminary results for the biooptical in-situ characterization of the investigated area,
as a contribution to the main “FLEXSense Campaign”
goal based on the atmospheric correction for theSentinel-3 - FLEX tandem mission and to the evaluationof the “FLuORescence Imaging Spectrometer” (FLORIS)
applicability to the coastal marine environment
features.

(Switzerland). The data set comprises concurrent
measurements with in situ (Fluorescence Box, FloX),
airborne (HyPlant) and spaceborne (Sentinel-3A,-3B)
spectrometers. We apply several retrieval methods
including the fluorescence line height method, adifferential absorption spectroscopy approach, and an
inversion of a bio-optical model. We quantitatively
assess the suitability of the retrieval methods crossobservational scales to disentangle reflected fromemitted fluorescence light and to compensate foratmospheric disturbances. We discuss possibilities andpotential limitations of the individual retrieval
strategies.
Our results and insights will guide the development ofnovel and robust SIF retrieval approaches for inland andcoastal waters. This may also potentially lead to a water
quality product for FLEX. The availability of more
efficient techniques in obtaining SIF will be beneficial
for water quality monitoring (e.g. harmful algal bloom
detection) and will facilitate ecological studies (e.g.
identification of phytoplankton functional types,
primary production assessments). Finally, our results
will further demonstrate the significance of FLEX
mission data for aquatic research and its many
applications.

************************

Retrieval of sun-induced fluorescence in opticallycomplex waters: Insights from observations of theSentinel-3 tandem phase

Gupana R1,2, Odermatt D1, Damm-Reiser A1,2

Eawag, Swiss Federal Institute of Aquatic Science andTechnology, 2Department of Geography, University of
ZurichSun-induced fluorescence (SIF) from phytoplankton isrecognized for its good correlation with the water
quality parameter chl-a concentration and has been awidely used parameter in in-situ and laboratory
measurements particularly for ecological studies. The
presence of in-water constituents aside fromphytoplankton, however, challenges the retrieval of
sun-induced fluorescence (SIF) in optically complex
waters. Further, high spectral resolution in the red-NIR
region spectral is necessary to extract the full SIF
emission shape in high detail and increase the accuracyof SIF retrievals, which is not available in multispectral
sensors (e.g. MODIS, MERIS, Sentinel-3 OLCI). The
upcoming Fluorescence Explorer (FLEX) mission
currently under development by the European Space
Agency provides hyperspectral capability between 500780nm and can possibly be used to advance SIF
retrievals and therefore water quality monitoring ofcoastal and inland waters.
1************************A new SICF retrieval algorithm for water bodies andthe implementation possibilities for the FLEX/S3
tandem mission.
Tenjo C1, Ruiz-Verdú A1, Van Wittenberghe S1, Sabater
N1, Delegido J1, Moreno J1
1
Universitat de València
The modelling of the spectral behaviour in bodies ofwater is not trivial, due to the high spectral variability ofthe different water compounds. Similarly, the Sun
Induced Chlorophyll Fluorescence (SICF) signal
produced by phytoplankton and leaving the water bodyis affected by these different water compounds.
To separate to the SICF emission from the peak
produced by the combined effects of water andphytoplankton absorption a new retrieval algorithm
was developed, as improvement to the commonly used
Fluorescence Line Height (FLH) method. Here, twoconcepts of Remote sensing reflectance (Rrs) has been
used: (1)real water-leaving reflectance (Rrsr) corresponding to
Rrs without SICF contribution and (2) water-leaving
apparent reflectance (Rrsapp) corresponding to Rrs
with SICF contribution. In nature, only (Rrsapp) is
detectable at water surface level. Because of this, aThis study aims to investigate different retrieval
techniques for phytoplankton fluorescence in opticallycomplex waters and their potential to distinguishdifferent algal groups. We use a unique data set
obtained between June – August 2018 in the Tyrrhenian
Sea (Italy) and in the inland water site Greifensee25

************************

methodology able to separate Rrsr from Rrsapp is
proposed. We estimated Rrsr based on normalized
Rrsapp at 780 nm (Rrsappn780) by using spectral ranges
that are not affected by the emitted SICF signal. Fromsimulated data we observed that Rrsappn780 can bemodelled as a polynomial of 8 degrees expression. Also,a strong correlation between the spectral range insideof the SICF emission signal and the both spectral ranges
outside of the SICF emission signal was corroborated.
Hence, by finding three adjust points inside of the SICF
emission spectral range based on (1) the points outside
the SICF range and (2) the Rrsappn780 polynomial. To
estimate the adjust points inside of the SICF emission
spectral range, Machine Learning Regression Algorithm(MLRA) methods and LookUp Table Based Inversion(LUT-BI) were used. A validation was performed using
simulated data.
To corroborate the application of the newly proposed
algorithm for the FLEX-Sentinel 3 mission, the simulated
database was convolved to the spectral response of
OLCI and both the FLH and the new algorithm were
tested. The new algorithm obtained relative errors withrespect to the true SICF less than 20% in 70% of thecases of SICF estimated at 685 nm and in 80% of thecases for the estimation of spectrally integrated SICF
(661-710 nm). The FLH method, on the other hand,showed relative errors less than 20% only in the 11% of
the cases for the estimation of spectrally integrated
SICF (661-710 nm).
Additionally, the implementation requirements for thealgorithm in the FLEX-Sentinel 3 mission were
evaluated, considering (1) the Signal-to-Noise Ratio(SNR) of the sensor and (2) the effects of theatmospheric correction. According to this study weobserved that (1) The impact of the type of atmosphereaffects to the ρ wapp retrieval is low comparing to the
instrumental noises effects, but is evident that in thecase of a dense atmosphere the retrieved Rrsapp isnoisier than in the case of a light atmosphere.
(2) The FLuORescence Imaging Spectrometer (FLORIS)
SNR is enough to obtain a good signal of bodies ofwater, as long as the Rrsapp levels are high enough toovercome the levels of instrumental and atmosphericnoise. This will depend as much on the irradianceconditions as on the composition of the water. In
conclusion, the new proposed SICF retrieval shows
good results under the condition a good FLEX
atmospheric correction can be performed, requiring ahigh water body reflectance, optimal atmosphericconditions and a very accurate ISRF modelling. This
research opens the door to higher precision and moreexhaustive studies of the behaviour of phytoplankton
and its photosynthetic activity at the local and global
scale.

26

Analysis of high frequency of remote sensing
reflectances in optically complex waters for the next
generation of hyperspectral sensors

sensitivity analysis on SICF signal) and bio-opticalmodelling parameterized with the specific inherent
optical properties. The inversion of Rrs data fromWispStation in Lake Trasimeno showed that chl-aconcentrations showed variations higher of 100%
during the day. The ROX data in Lake Maggiore allowed
to evaluate the presence of a small peak due to the SICF
in late afternoon data.
Rrs data were then resampled based on radiometricsettings of the satellite sensors that are (or will be)
crucial for investigating phytoplankton properties ininland waters such as: Sentinel-3A OLCI, Sentinel-3B(with the OLCI sensor working in ‘FLEX modality’ with
about 50 bands, rather than 21), FLEX and PRISMA
hyperspectral missions. The analysis aims to adapt thestate-of-theartalgorithms
forretrieving
biogeochemical parameters to the next generation of
hyperspectral satellite (apart a continuous testing withOLCI).

Bresciani M1, Giardino C1, Hommersom A2, Manca D3,

Julitta T4, Cesana I5, Cogliati S5, Colombo R5
Cnr-irea, 2Water Insight, 3Cnr-Irsa, 4JB Hyperspectral,
5
Università Milano Bicocca
The complex aquatic ecosystems, such as lakes, aregenerally characterized by a high degree of spatial andtemporal changes. In particular, hourly and daily
dynamics are evident due, for examples, to thegrowth/decrease of phytoplankton depending on lightavailability and to the variation of the suspended solids
in wind-induced resuspension of the bottom sediments.
Such a variability is then changing depending on
location, so that variation in spatial patterns is also atypical feature of these ecosystems.
Satellite images have been used widely since many
decades to observe and to understand spatial andtemporal variability of water constituents, while theexploration of hourly temporal variability is still limited
to geostationary sensors, whose spectral and spatial
resolutions are anyway limited for resolving theoptically complexity of inland waters. To fill this gap, in
this contribution we present the results obtained byacquiring Remote Sensing Reflectance (Rrs) from two
hyperspectral spectroradiometers mounted on fixed
platforms and / or on floating buoys. These sensors
allow to gather continuous measurements during the
day and for several consecutive days from two different
yet comparable devices. A set of Rrs measures weretaken by a WispStation (manufactured by Water
Insight) in Lake Trasimeno (in the April-September 2018
range). The system measures every 10 minutes theradiance and irradiance in the spectral range of 350-900
nm with a spectral resolution of 3 nm. The set-up isbased on an automatic system so that the instrument
detect the water surface at optimal azimuth angles formost of the day. A second set of Rrs spectra was insteadacquired by a ROX sensor (manufactured by JB
Hyperspectral devices) operated on a floating buoy in
Lake Maggiore at the end of June 2018. The ROX system
is assembling Ocean Optics spectroradiometers and it
operates in the range 400–950 nm with a spectral
resolution of 1.5 nm and with an acquisition time of 1
minute.
Rrs data collected by both systems were pre-processedfor quality control and mostly for removing glint. The
noise-free data were then analysed to investigate
phytoplankton types mostly in terms of Chlorophyll-a(Chl-a) concentrations, phytoplankton pigments and of
Sun Induced Chl-a Fluorescence (SICF). This analysis was
performed based on forwarded simulations of theradiative transfer code Hydrolight (mostly for a1************************

Modelling Environmental Impacts And Adaptation On
Sustainable Marine Ecosystems In the Gulf-of-Guinea
Coast

Akande S1Federal University Of Technology Akure
The global climate change influence marine animals
through the ocean warming, acidification andoxygenation. This has affected the socioeconomic
aspect of acquaculture through changes in seawaterchemistry, sediment transport, decrease in seawater
pH (acidification) etc. The study was conducted in the
Gulf of Guinea region of the North Atlantic which
stretches from the Senegal in the West to Gabon to theSouth-Eastern part of Africa. It is home to a large
number people and economic activities with over fifty(50) million African population. In order to ensure thepreservation of preserving natural resources andmarine ecological features, a modified methodologicalapproached was developed to evaluate risk of marine
ecosystem.
Monthly annual sea surface temperature data wereobtained the National Oceanic and Atmospheric
Administration (NOAA) and Advanced very-highresolution radiometer (AVHRR) over the Gulf-of-Guinea
region between 1972 to 2017 (45 years) were analysed
in relation to acess the long term trend of ocean heattransport and changes in ocean circulations within the
study area High resolution Sentinel-2, ALOS PALSAR and
ASTER satellite images were acquired and processed
coastal vegetation, erosion assessments, extract
emissivity and temperature and spatial modelling, thatare in combination with historical estuary evolution and127

field observation was applied for effective management
and conservation the ecosystem features of the area. It
was then observed that the climate change impacts on
aquaculture is highly predominant in tropical andsubtropical climatic regions of the world, thus there isneed to assess the implications of future scenarios interms of climate change and research development in
the areas of aquaculture. The recommendations fromthis research thus improve strategies and policy
measures needed to fight the observable and projectedclimate change impacts on fisheries and aquaculture, so
as to protect the livelihoods of the fishing communities
and food security. Finally, Integrating the needs of fish
farmers and acquaculturists into adaptation planning isvery essential.

************************

28

and provide necessary information for thecalibration/validation of multi-source remote sensing
data and products.

In situ measurement offluorescence II************************
Chlorophyll Fluorescence Calibration/Validation
Measurements at the USDA Beltsville researchcornfield over 20 years

Middleton E1, Campbell P2, Huemmrich K2, Landis D3,

Ground-based fluorescence measurements andvegetation dynamics across different ecosystems

Zhang Q4, Ong L5, Hom M5, Corp L5, Sabater N6, Cogliati
S7, Alonso L6, Russ A8, Kustas W8, Daughtry C8
1
NASA Goddard Space Flight Center, 2University of
Maryland Baltimore, 3GST, 4Universities Space
Research Assoc., 5Science Systems and Applications,Inc., 6University of Valencia, 7University of Milan,
8
Unites States Dept. of Agriculture
This presentation will summarize the evolution of field
and laboratory measurements that comprise our
proximal sensing protocols for fluorescence and plantbiophysicalparameters(e.g.,
maximum
photosynthesis, chlorophyll content) at the USDA
research site in Beltsville, MD, USA. The methods andmeasurements we made over the past two decades
evolved for collecting consistent leaf and canopy
measurements for corn (maize) crops in different years
and with different soil nitrogen augmentation levels.
We also highlight results from one summer season
when we tracked canopy responses during a droughtfor corn stands provided both water and nitrogen
treatments. We describe the development of a 10 m
tower system for our custom multi-instrument andmulti-angle optical system, FUSION, to survey the
canopy along with an eddy covariance tower to track
the carbon dynamics. In the past two years, we added
a D-FloX system and complementary in-situ leaf-levelmeasurements from a MONItoring Pulse Amplitude
Modulated (Moni-PAM) system, supplemented byspectrally resolved FluoWat collections. We provide
both diurnal and seasonal trends for red and far-red
solar-induced fluorescence (SIF) and reflectance indices(e.g., PRI, NDVI), and demonstrate how we used our
combined measurements as input to the SCOPE model
to estimate light use efficiency and gross primary
production.

Colombo R1, Boschetti M2, Celesti M1, Cogliati S1,

Drusch M3, Genesio L4, Julitta T5, Pilar Martin M6,
Migliavacca M7, Miglietta F4, Panigada C1, Rascher U8,
Rossini M1, Schüttemeyer D3, Siegmann B8, Tagliabue
G1
1
University Of Milano Bicocca, 2CNR, Irea, 3European
Space Agency, 4CNR, Institute of Biometeorology, 5JB
Hyperspectral Devices , 6CSIC, 7Max Planck Institute for
Biogeochemistry, 8Forschungszentrum Jülich GmbHIn this contribution, we present activities and groundbased results obtained in recent campaigns conductedin the context of the future spaceborne FLuorescence
EXplorer (FLEX) mission. In summer 2018 several testsites, encompassing agricultural and forest ecosystems,
were investigated at field, airborne and satellite level todemonstrate the feasibility of fluorescence retrievals
for a better understanding of the functioning ofvegetation from space.
All sites were equipped to acquire in situ measurementsof top of canopy radiance, atmospheric properties andeddy covariance measurements. Reflectance and suninduced fluorescence at ground level were estimatedstarting from spectral data collected with the FloX
system, to get both continuous time series across fullvegetative periods and to characterize the spatial
representativeness of the sites. At the Italian
agricultural site, we sampled different crops fromFebruary 20th up to 15th September to collectbiophysical vegetation parameters and solar induced
fluorescence in different phenological conditions andwith different irrigation scheme. We particularlypresent the results for the retrieval of the full
fluorescence spectra and the evaluation of different
fluorescence metrics, towards FLEX Level 2 products,
for better interpreting time courses and spatial pattern
dynamics of fluorescence of the investigated land use
and cover. Ground-based spectrometers and theestablishment of an international fluorescence network
can offer several benefits toward a better
understanding of terrestrial ecosystems, animprovement of operational atmospheric corrections,************************

29

Effect of the canopy architecture on the diurnal timecourse of sun-induced chlorophyll fluorescence andderived indicesInstitute of Bio- and Geosciences, IBG-2: Plant
Sciences, Forschungszentrum Jülich GmbH , 2Universityof Valencia, 3University of Twente, Faculty of GeoInformation Science and Earth Observation (ITC),
4
Institute of Ecology, University of Innsbruck,
5
Meteorology Department, Poznan University of Life
Sciences, 6Sustainable Agro-Ecosystems andBioresources Department, Research and Innovation
Centre, 7Department of Earth and Environmental
Sciences, University of Milano-Bicocca, 8Department ofAgricultural, Food, Environmental and Animal Sciences,
University of Udine, 9Institute of Biometeorology,
National Research Council (CNR- IBIMET), 10JB
Hyperspectral Devices UG, 11Foxlab Joint CNR-FEM
Initiative, 12IMèRA, Institut D‘Etudes Avancés del’Universitè Aix-MarseilleNovel measurement techniques to estimate suninduced chlorophyll fluorescence (F) together with thehyperspectral reflectance (R) have become available inrecent years. A relevant question is whether the
combined use of these measurement techniques canhelp to quantify the productivity of different cropvarieties. We investigated the F and R of two varietiesof Soybean (Glycine max (L.) Merr.), a chlorophylldeficient (MinnGold, chlorophyll (Cab) of 9.52±0.98 mg
cm-2) and a non-chlorophyll deficient (Eiko, Cab of
46.49±5.59 mg cm-2) variety, in order to explain
similarities and differences in photosynthesis and lightuse efficiencies. We were particularly interested in
explaining the light absorption and fluorescenceemission at photosystem level, which are bothindicators of photosynthesis.
1

Goulas Y1, Moya I1, Ounis A1

Dynamic Meteorology Laboratory
Remote sensing of sun-induced fluorescence (SIF) fromterrestrial vegetation is the subject of intense research,with the aim to evaluate photosynthetic efficiency atlarge scales under various environmental conditions.
The FLEX mission is specifically designed for SIF
measurements and will provide fluorescence products
from space at an unprecedented spatial and temporal
resolution. Indeed, chlorophyll fluorescence (ChlF)
emission is tightly linked to the photosynthetic
mechanisms as it emanates from the energy absorbedby photosynthetic pigments and competes withphotochemical conversion. Under various stressconditions, acclimation of plants results in an increased
dissipation pathway (i.e. non photochemical
quenching) that affects the stationary ChlF yield underambient light. Active measurements of ChlF diurnal
cycle at leaf or canopy level showed a significant
decrease of the fluorescence level in the middle of theday upon water stress, compared to control conditions.
However, the diurnal cycle of SIF also includes theabsorbed photosynthetically active radiation (APAR),
which results in the complex interaction of incoming
sun radiation and canopy architecture. The radiativetransfer of fluorescence in the canopy should also betaken into account. In this study, we investigate theeffect of canopy architecture on the diurnal cycle of SIF
using a modeling scheme coupling Modtran 4,
FluorMODleaf and SAIL. Different normalization
procedures are evaluated according to canopy
structure parameters (leaf area index, leaf angular
distribution, chlorophyll content), with the aim todiscriminate between water stressed plants and control
and we propose a new fluorescence-based index forwater stress detection.

1

Our measurements of top of canopy (TOC) F and R, andcanopy level gross primary productivity (gas exchangechambers) showed that despite the higher Cab of the
Eiko both varieties present similar canopy-scale grossprimary production, and the ratio of carbon uptake tolight absorption ratio was higher in the MinnGold. We
further retrieved parameters for the ‘Soil-CanopyObservation of Photosynthesis and Energy fluxes’ model(SCOPE) from leaf and (TOC R, and used SCOPE tocorrect F for reabsorption of fluorescence in the canopy.
The emission of fluorescence in the photosystems
appeared to be similar in both varieties. This indicatesthat the higher light absorption in the Eiko as comparedto the MinnGold is compensated by higher nonphotochemical quenching (NPQ) due to light saturation.
Our findings demonstrate that the combination of F andhyperspectral R can help better understand andquantify the light reactions of photosynthesis in cropvarieties.

************************

Correcting for Sun Induced Fluorescence reabsorption– from leaf to canopy – in chlorophyll-deficient andgreen soybean plants
Ciavatta S.1, Kay S.2, Saux-Picart S.3, Butenschön M.2,
Cendrero-Mateo M1,2, van der Tol C3, Sakowska K4,5,6,
Celesti M7, Schickling A1, Alberti G8,9, Alonso L2, Burkart
A10, Cogliati S7, Colombo R7, Delle Vedove G8, Julitta
T10, Juszczak R5, Moreno J2, Muller O1, Panigada C7,
Peressotti A8, Rademske P1, Rossini M7, Tagliabue G7,
Vilfan N3, Yang P3, Miglietta F9,11,12, Rascher U1************************

30

functioning. Established active and passive remotesensing approaches (e.g. using Sentinel-1, -2 and -3
mission data) provide a diverse set of information onplant’s biochemistry and structure. The development ofEuropean Space Agency’s upcoming Fluorescence
Explorer (FLEX) mission will complement existingobservational capability and, for the first time, allow
assessing functional traits representing actual plant
mediated gas exchange processes (i.e. net CO2
assimilation (A), transpiration (T)).

Linking fluorescence andecosystem processes I water cycle

The relationship between sun-induced fluorescenceand transpiration is determined by atmosphericconditions and less by vegetation properties

The development of FLEX mission data products
representing plant’s gas exchange requires combining
remote sensing measurements with established in situ
observations of gas exchange (e.g. eddy covariance (EC)measurements). Combining both observational
approaches, however, is an unsolved scientific problem
and caused by fundamentally different samplingstrategies of both techniques. While EC measurements
represent a spatially varying area of a verticallyintegrated canopy, remote sensing measurements
represent the upper leave layer of a fixed canopy
region. Further, the relation of both observations varies
in time and space depending on how the upper canopy
layer is coupled with or decoupled from the verticallyintegrated canopy.

Maes W1, Miralles D1, Pagan B1, Martens B1, Gentine

P2, Steppe K4, Verhoest N1, Dorigo W3
1
Laboratory of Hydrology and Water Management,
Ghent University, 2Department of Earth andEnvironmental Engineering, Columbia University,
3
Department of Geodesy and Geoinformation, TU
Wien, 4Laboratory of Plant Ecology, Ghent University
Satellite observations have revealed that relationships
between sun-induced fluorescence (SIF) and latent heat
flux (lE) are at least as strong as those between SIF and
GPP. This could provide a new means to estimatetranspiration more directly and accurately from space.
In this research, we used the Soil Canopy Observationof Photosynthesis and Energy fluxes (SCOPE) model tobetter understand the drivers of the relationshipbetween SIF and lE. We calibrated SCOPE for eachavailable day of each individual site of the
FLUXNET2015 database, using MODIS data and eddy
covariance observations of GPP and lE and calculated
SIF. This yielded a dataset of over 50k realistic
simulations of 10 different biomes. Whereas the SIFGPP relationship was, as expected, mostly influenced byvegetation properties, the SIF-lE relationship was hardly
influenced by these vegetation properties, including
even carbon metabolism, but was largely determinedby atmospheric conditions, i.e. net radiation, airtemperature and vapour pressure deficit. Thisfacilitates a more direct estimation of transpiration overlarge scales, making use of upcoming advances insatellite SIF.

In this study, we provide a tomographic perspective on
the gas exchange of a forest canopy. We use 3D
radiative transfer models, ecohydrological models, insitu
fluorescencemeasurements
andmicrometeorological observations (including EC
measurements) to simulate 3D fields of transpiration T
and A. We analyze these 3D fields to quantify the
relation of T and A from the upper canopy (remotesensing perspective) with the vertically integrated T and
A (EC perspective). We assess the impact of canopy
structure and environmental conditions on observed
relationships. We identify strategies to compensate fora possible footprint mismatch and to account for the“remote sensing bias” when assessing 3D forest
canopies. Our findings provide substantial insights tofacilitate the harmonization of remote sensing and insitu gas exchange measurements. Results will guide thedefinition of novel FLEX mission data products and of
optimal validation strategies for such products.

************************

Tomography of forest gas exchange: Implications forthe development of novel FLEX mission data products

Damm A1,2, Kückenbrink D1, Morsdorf F1, Paul-Limoges************************

E1, Haghighi E2
1
Department of Geography, University Of Zurich,
2
Eawag
Comprehensive assessments of functional, biochemicaland structural plant traits is pivotal to assess the statusof plants and reveal subtle interactions and feedbacks
between environmental forces and ecosystem

31

Investigating the potential of sun-induced chlorophyll
fluorescence to advance estimates of ecosystemtranspiration

contribution of SIF and the need of additional
environmental factors for reliable estimates of actual Tr
from regional to global scale. Our study is important forthe definition of higher level FLEX mission products
facilitating estimates of Tr dynamics in space and time.

Ahmed K1, Paul-Limoges E1, Damm A1,2

Remote Sensing Of Water Systems, Department Of
Geography, University Of Zurich, 2Swiss Federal
Institute of Aquatic Science and Technology (EAWAG)
Transpiration (Tr) is an important and complex plant
physiological process in terrestrial ecosystems andsignificantly impacts the global water and energybalance. Assessing the dynamics of Tr has versatile
implications to understand causes of water scarcity, toadvance the understanding of interactions andfeedbacks between global climate change andecosystem functioning, to assess plant water use
efficiency for optimized agricultural management, andto exploit the coupled carbon and water cycle.
Nevertheless, spatio-temporal assessments of Tr using
models or Earth observation (EO) informed approaches
are still uncertain due to the complexity of Tr,
limitations in existing methodology, and lack ofobservational approaches only accounting for potential
rather than actual Tr. New pathways arise from thedevelopment of ESA’s upcoming Earth Explorer mission
Fluorescence Explorer (FLEX), which will provide global
measurements of sun-induced chlorophyll fluorescence(SIF). SIF is considered the most direct measurement ofplant photosynthesis and possibly allows informing
approaches to estimate actual Tr.
In this study, we assess a possible contribution of SIF toadvance cross scale Tr by comparing estimates ofpotential and actual Tr and its dynamics under theextremely warm and dry 2018 summer in Europe. We
apply a mechanistic approach combining processmodeling (i.e. a combination of the Penman-Monteith(PM) and the Ball-Berry-Leuning (BBL) model) andmulti-source EO data (i.e. Sentinel-3, European Centre
for Medium-Range Weather Forecasts (ECMWF)) to
calculate actual and potential Tr. In particular, wevaried the parameterization of the canopy surface
resistance with a greenness based estimate ofphotosynthesis (potential Tr) and a SIF surrogate (actualTr). Estimates of potential and actual Tr were validatedwith flux data from eddy covariance sites in Europe.
Further, we quantify dynamics of Tr under different
climatic conditions using monthly time series of
selected study sites in southwestern Europe over two
years, the drought year 2018 and the baseline year
2017.
Our results reveal complex patterns of Tr dynamics(potential and actual) over two years in Europe. We
discussthese
results
considering
possiblesuperimposing environmental factors for different
ecosystem types. Obtained insights show the possible1************************The mechanistic link between transpiration and suninduced chlorophyll fluorescence in a mixed forest:
Insights from the 2018 European drought

Paul-Limoges E1, Damm A1,2

Department of Geography, University of Zurich,
Eawag, Swiss Federal Institute of Aquatic Science andTechnology
Plant transpiration (T) accounts for 60 to 80% of
terrestrial evapotranspiration, thereby having adominant influence on the global water cycle. As
temperatures increase and more extreme droughts are
expected to occur, it is unclear in which direction T will
evolve in our ecosystems; T could, for example,
decrease due to stomatal closure leading to anincreased warming or T could be stimulated by theincreased ability of the atmosphere to hold more water
vapour leading to a cooling effect. In order tounderstand these vegetation response dynamics andinform models, measurements are needed at
ecosystem-level to quantify the evolution in T.
However, consistent T measurements at ecosystemlevel are currently lacking. The mechanistic linkage
between photosynthesis and T by stomatal
conductance opens new possibilities to inform T
estimates by sun-induced chlorophyll fluorescence(SIF), the most direct remote sensing measurement ofplant photosynthesis.
1
2

In this study, we apply a novel approach using
concurrent below and above canopy eddy covariance(EC) measurements in a mixed deciduous forest in
Switzerland to partition water vapour fluxes into
evaporation and T, based on the coupling of the layers
and on the origin of the water vapour sources. We thenexplore the mechanistic link between the T-derived and
SIF retrieved from continuous tower-based FloX
measurements, as well as their link to stomatal
conductance, water stress, and other environmental
factors. We found that, in our mixed forest, midafternoon reductions in T occurred during periods ofhigh vapour pressure deficit in summer. T and SIF
similarly declined during the drought of the 2018
summer, due to the water stress imposed on the trees.
Our results contribute to a better understanding of T
dynamics during drought conditions as well as their link
to SIF. Provided insights will guide further

32

developments of SIF informed modelling approaches toestimate T across spatial scales.

difficulties in parametrization of the LUE terms; lightuse efficiency of photosynthesis (LUEp) and efficiencyof fluorescence emission (LUEf), as well as Fesc, limits
the applicability of this method.

************************In this contribution we make use of data collected at the
research site Majadas de Tietar, a Mediterranean
grassland manipulated with nitrogen and phosphorus.
With a combination of processes-based soil-vegetationatmosphere transfer modelling (SCOPE model) and data
driven analysis (relative importance analysis, and pathanalysis with intervention), we unravel the processes
and causal relationship that are at the base of the GPPSIF relationship. Additionally, via path analysis weunderstand how different nutrient conditions alter themechanistic processes that drive both GPP and SIF.

Linking fluorescence andecosystem processes II carbon cycle

Mechanistic processes driving Sun-Induced
Fluorescence and Gross Primary Production undernutrient manipulation

We show that functional traits such as leaf nitrogencontent influence SIF emission and GPP in a rather
indirect way, being the nitrogen effect on SIF emission
mainly mediated by absorbed photosynthetic active
radiation (APAR) and surface temperature. On the other
hand, structural variables affect SIF emission bymodulating APAR and influencing SIF by varying Fesc.

Martini D1, Pacheco-Labrador J1, Perez-Priego O1, van

der Tol C2, El Madany T1, Julitta T3, Rossini M4,
Reichstein M1, Moreno G5, Christiansen R6, Carrara A7,
Migliavacca M1
1
Max Planck Institute For Biogeochemistry, 2Twente
University, 3JB hyperspectral devices, 4University of
Milano Bicocca, 5Universidad de Extremadura,
6
University of Copenhagen, 7Centro de Estudios
Ambientales del Mediterráneo
Sun induced fluorescence (SIF), the radiation flux
emitted by plant chlorophylls molecules in the 650-800
nm spectral window, is considered an indicator ofphotosynthetic performance. Recently it has beenshown that SIF can track changes in light use efficiency(LUE), and therefore it is a good predictor of grossprimary productivity (GPP) at various scales, fromleaves and ecosystem to regional and global scale.

As the GPP-SIF relationship across nutrient treatmentshows significant changes on N fertilized plot, we show
which are the main drivers and the most important
processes that mechanistically influence therelationship. In particular in the first year of fertilization,changes in GPP-SIF were mediated by a combination offunctional and structural variability, whereas in thesecond year, changes in plant functional typeabundances cause a strong structural variation that inturn influences SIF by means of higher APAR and Fesc.
This contribution advances the knowledge of the highly
complex dynamics involved in the GPP-SIF relationship.
In depth understanding of the mechanistic processes isrequired to fully take advantage of the increasingly
prevalent SIF data streams

Although SIF has been successfully used to predict GPP
in various ecosystems, the mechanistic link between
GPP and SIF remains not fully understood, andespecially the effect of functional and structural traits
on SIF at the canopy scale remains an active area of
research.

************************

SIF is emitted by the whole canopy, but only a fractionof the total emission is observed with remote sensing
techniques. The escape probability of SIF (Fesc) controls
the amount of SIF scattered by the canopy and is
integral to separate the effect of canopy structure andfunction on the fluorescence signal.
Approaches based on the LUE equation are widely used
to model the relationship between GPP and SIF,
however a lack of process understanding as well as

33

Partitioning the structure and photosynthetic
pathway for scaling solar-induced fluorescence togross primary production from satellite observations

Improvements in GPP spatio-temporal patterns
simulated with the ORCHIDEE terrestrial biospheremodel resulting from the assimilation of OCO-2 solarinduced fluorescence products and the developmentof a mechanistic SIF model

Zhang Y1, Zhang Z1

Nanjing University
Photosynthesis by terrestrial vegetation absorbs half ofanthropogenic CO2 from the atmosphere. Large-scale
photosynthesis quantification has remained challenged
due to the lack of sufficiently accurate remote sensing
proxies. It is therefore critical to accurately measure
photosynthesis at the spatial scale of ecosystem toglobal. Remote sensing of sun-induced chlorophyll
fluorescence (SIF) has been shown a good indicator ofvegetation photosynthesis or gross primary production(GPP) across diverse scales. Along with the
breakthroughs of global retrievals of SIF from spaceborne sensors, exploitation of SIF in improving theestimation of terrestrial GPP became a very relevant
and active field. However, it remains unclear how theslopes of GPP-SIF relationship vary across biomes due
to canopy structure and physiological factors due tophotosynthetic pathway, especially as a result of lacking
long-term field measurements of SIF and scalemismatch between satellite SIF data and flux tower GPP
estimates. In this presentation, we present a synthesisof field continuous measurements of SIF across biomes
which is used to unravel the GPP-SIF relationships
across different biomes together with improved SIF
retrievals from OCO-2. We find that the slopes of raw
SIF with respect to GPP are significant different among
biomes, which we attributed both to canopy structuraleffects as well as to differences in photosynthetic
strategies. After accounting for the escape effects from
canopy structure with the corresponding BRF, however,a photosynthetic-pathway dependent GPP model from
SIF emerges for C3 and C4 plants that allows for simple
calculation for terrestrial photosynthesis at the global
scale. This results are supported by process-basedmodel simulations. With the new GPP models fromadjusted SIF with the corresponding NIR BRF for C3 andC4 plants, fully observation-based and independent
global GPP estimates (126.80±1.22 PgC/year) are
derived for the period of 2015-2017 from OCO-2 SIF
retrievals; this falls within the range of current
terrestrial biosphere models and up-scaled flux tower
estimates. Our results indicate that the slopes of GPPSIF relationship across biomes are jointly controlled bycanopy structure and physiological factors, and aphotosynthetic-pathway dependent SIF-based GPP
model provide a simple and independent constraint onterrestrial photosynthesis at the global scale.

1

Bacour C1, Maignan F2, MacBean N3, Porcar-Castell A4,

Flexas J5, Frankenberg C6, Vuichard N2, Peylin P2,
Bastrikov V2, Chevallier F2
1
Noveltis, 2Laboratoire des Sciences du Climat et del'Environnement, 3Department of Geography, Indiana
University, 4Department of Forest Sciences, University
of Helsinki, 5University of the Balearic Islands,
6
California Institute of Technology
By offsetting about one fourth of carbon dioxide (CO2)emissions released by anthropogenic activities into theatmosphere, terrestrial ecosystems plays a pivotal rolefor climate. The assimilation of CO2 by photosynthesisthat occurs in leaf chloroplasts is largely compensatedby ecosystem respiration and fires that release some of
the CO2 back into the atmosphere. As highlighted by
the large spread in dynamic global vegetation model(DVGM) simulations relative to the spatio-temporal
patterns of the terrestrial gross primary productivity(GPP), large uncertainties remain in our understandingof the carbon sequestration in land surfaces. Part ofthese uncertainties result from unknown or poorly
calibrated parameters in DGVMs. Over the past decade,the use of space-borne retrievals of solar-induced
fluorescence (SIF) as a proxy of GPP at large temporaland spatial scales has grown in importance. Their use
for constraining DGVMs implies that these models areable to simulate SIF observables and represent thefunctional links between GPP and SIF.
In this study, we present the development of a SIF
observation operator in the ORCHIDEE DGVM (Krinneret al., 2005). It relies 1) on a novel parameterization of
NPQ as a function of temperature, APAR and thenormalized quantum yield of photochemistry (i.e.
ratioed by the maximum quantum yield ofphotochemistry), to simulate the regulation of the PSII
fluorescence quantum yield at the leaf level, and 2) a
parametric simplification of the SCOPE model toemulate the radiative transfer of chlorophyll
fluorescence to the top of the canopy.
We then apply a Bayesian assimilation framework to
assimilate monthly OCO-2-SIF product at 0.5° over theperiod 2015-2016 and hence calibrate ORCHIDEE overan ensemble of pixels for all vegetation plant functional
types (PFTs). Through the optimization ofphotosynthesis
andphenological
ORCHIDEE
parameters mostly, the feedback on the simulated GPP
is considerable with a decrease of the global budget by
33 GtC.yr-1 over the 1990-2009 period (from 162************************
34

GtC.yr-1 with the standard model parameters to 129
GtC.yr-1 after assimilation). Although the optimized
global GPP budget gets in close agreement with that ofindependent FLUXCOM GPP products (Tramontana etal., 2016) (121 GtC.yr-1 in average over the same
period), the spatio-temporal distribution of the
improvement of ORCHIDEE relative to both OCO-2-SIF
observations and FLUXCOM-GPP estimates show
contrasted results between ecosystems. Indeed, ourassimilation framework results in opposite variations in
the modeled SIF and GPP for temperate and boreal
deciduous forests, contrary to other PFTs. This suggest
a biome dependency of the SIF-GPP relationship, likely
through differences in the radiative transfer regime,that needs to be resolve to enhance the observational
constraint brought by space-borne SIF products onvegetation productivity. We discuss the benefits ofusing SIF data to constrain DGVMs with regards to otheravailable observations.

nutrient availability on ecosystem functioning (e.g.
photosynthesis and water use efficiency) is pivotal.
Reflectance based spectroscopy can be used to directly
infer variations in biochemical and partially structuralchanges of vegetation under different meteorologicaland environmental conditions. Besides, novel
measurements of sun-induced chlorophyll fluorescence(SIF) both in the red and far-red regions open new
pathways to non-invasively quantify dynamic changes
in ecosystem functioning. However, the mechanistic
link between photosynthesis, water use efficiency and
SIF under different environmental conditions is notcompletely understood yet.
In this contribution we will synthesize the information
coming from a series of campaigns at different eddy
covariance sites as well as climate and nutrient
manipulation experiments. We collected data from 1) a
nitrogen (N) and phosphorous (P) manipulation in a
Mediterranean grassland; 2) and a climate
manipulation experiment, with elevated CO2 (+0, +300ppm), temperature (+0, + 3 ºC) and water stress (rainmanipulation with shelters), and the combination of thethree factors; 3) and various sites where eddy
covariance data and SIF were measured
simultaneously. These sites include a Mediterranean
tree grass ecosystem with different nutrient availability,
a semi-arid pine forest, and an orchard. The sites
experienced a series of drought events and/or a heatwave. The common set-up in all sites is the combined
measurement of CO2, Net Ecosystem Exchange (NEE)with subsequent partitioning of Gross Primary
Productivity (GPP), and evapotranspiration fluxes(either with chambers or with eddy covariancetechnique) with SIF in the O2-A (∼760 nm) and O2-B(∼687 nm) absorption features (obtained from the
Fluorescence BOX, JB Hyperspectral Devices).
Occasionally, the dataset is complemented by in situ
measured leaf traits such as nutrient content,
vegetation pigments and leaf area index (LAI)
measurements, maximum carboxylation rate (VCmax)
and maximum photosynthesis rate derived from leaf ACi curves, sap-flow measurements, carbonyl sulfide
measurements (OCS), and leaf isotopes signature
measurements (in particular δ13C). A model data
integration approach combining simulations performed
with the SCOPE model with the collected data was used
for process understanding.
Results show that elevated CO2 causes an increase ofboth GPP and SIF. SCOPE simulations show that theincrease in SIF emission can be explained by the
reduction of Non Photochemical Quenching (NPQ)
associated with the higher observed VCmax andintercellular CO2 concentration (Ci), which ultimately
leads to higher SIF than under ambient CO2. The N
fertilization induced changes in canopy structure (i.e.

Linking fluorescence andecosystem processes III

Sun-induced chlorophyll fluorescence to understandthe responses of terrestrial ecosystem functioning toclimate, environmental changes and extreme events

Migliavacca M1, Martini D1, Pacheco Labrador J1, Julitta

T3, Bahn M2, Burkart A3, Carrara A4, Cochavi A5,
Colombo R6, Damm A7, El Madany T1, Gerdel K2, Kitz F2,
Hammerle A3, Martin M8, Miglietta F9, Moreno G10,
Perez Priego O1, Rascher U11, Rossini M6, Sakowska K2,
Spielmann F2, van der Tol C12, Wohlfahrt G2, Yakir D5,
Reichstein M1
1
Max Planck Institute for Biogeochemistry, 2Universityof Innsbruck, 3JB Hyperspectral Devices, 4CEAM,
5
Weizmann Institute fo Science, 6University of Milano
Bicocca, 7University of Zurich, 8CSIC, 9CNR, 10Universityof Extremadura, 11Julich FZ, 12University of Twente
Understanding the responses of ecosystem functioning
to climate extremes and environmental changes is animperative question in global change ecology.
Therefore, the development of tools for monitoring theeffects of increasing temperature, water stress,
increasing atmospheric CO2 concentration, and35

changes in plant form abundances that influence leaf
inclination distribution function) and functional traits(e.g. nitrogen content per dry mass of leaves,
Chlorophyll ab concentration, VCmax), which lead to anincrease of SIF and GPP, but with a functional
relationship between the two variables and modulated
mainly by community structure (e.g. fraction ofgraminoids) and secondarily Vcmax. Surprisingly, weobserved a statistical significant effect of P on SIF
emission that we demonstrated to be related to theenhancement of the electron transport rate associatewith higher P content in leaves. GPP and SIF underwater stress treatments and combined CO2,
temperature stress, and water stress showed the
expected reduction, associated with an increase inwater use efficiency. This comprehensive dataset showsthat changes in species and therefore structure and leaf
contents induced by treatments can enhance SIF
sensitivity to vegetation responses, but have also a
confounding effect on the connection between SIF andfunctioning. Integrated approaches capable ofcharacterize plant structure, composition and function
together are necessary to truly understand the different
strategies of vegetation to face environmental change.
Less clear is the effect of heat waves and temperaturestress: while we overall observed reduction of GPP, theresponse of SIF and water use efficiency is very different
across vegetation types. We hypothesize that this
response might be related to different stomatalbehavior and strategies to cope with heat stress (and inparticular stomatal vs non stomatal regulation ofphotosynthesis), variations in the capacity of thevegetation to recover from high night-timetemperature, or that the temperature increase was notenough to stress the vegetation and go beyond the
optimal temperature.

biodiversity, which describes the variability of thoseplant traits that influence ecosystem functioning.
Changes in functional diversity can influence ecosystem
dynamics and stability. Thus, the capacity to monitor
reliably and consistently biodiversity in space and timeis essential. In the last few decades, surface reflectancedata were used with different degrees of success tomonitor changes in functional diversity from remotesensing data.
In this contribution, for the first time the potential of
sun-induced chlorophyll fluorescence in providing
information on functional diversity of terrestrial
ecosystems is investigated.
This was achieved exploiting high resolution airborne
images acquired with the FLEX airborne demonstrator
HyPlant. The HyPlant sensor consists of two modules:
one hyperspectral imaging spectrometer covering thespectral region from the visible to the shortwave
infrared and a second imager specifically designed for
fluorescence estimation in the red and near-infrared
regions.
The sensor was flown over forested areas characterized
by different species composition and stand age.
Different approaches to evaluate the functional
diversity based on reflectance and fluorescence data
were then assessed.
The heterogeneity across the study area was measured
using two different metrics related to the diversity: theShannon Entropy index, which takes into account therelative proportion of each pixels’ value, and the Rao’s
Q diversity which explicitly accounts for distancesamong pixels’ numerical values.
First of all, HyPlant raw data were georectified andatmospherically corrected to obtain top-of-canopy
radiance and reflectance. Maps of sun-induced
chlorophyll fluorescence at the far-red peak were thensuccessfully obtained (r2=0.73, p<0.001, compared to
top-of-canopy ground-based measurements acquired
synchronously with the overflight) using the Spectral
Fitting Method retrieval approach.
The entropy metrics were then calculated on maps offunctional plant traits, far-red fluorescence and NDVI,
which is the vegetation most commonly used in
ecology. Rao’s Q diversity performed better than the
Shannon’s index in characterizing the spatial
heterogeneity of the investigated forests. Notably, thefunctional diversity patterns obtained calculating Rao’s
Q diversity on the fluorescence map better related to
the functional diversity map used as a referencecompared to those obtained applying the entropy
metric on the NDVI maps. In particular, NDVI strongly
underestimates the functional diversity across thestudy area and particularly in the juvenile stands, where
the low entropy based on NDVI calculation shows that************************
Estimating functional diversity using sun-induced
fluorescence in terrestrial ecosystems
De Rossini M1, Tagliabue G1, Celesti M1, Cogliati S1,Colombo R1, Migliavacca M2, Rascher U3, Rocchini D4,
Schüttemeyer D5, Panigada C1
1
Department of Earth and Environmental Sciences,
University of Milano Bicocca, 2Max-Planck Institute for
Biogeochemistry, 3Institute of Bio- and Geosciences,
IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH
, 4University of Trento, Fondazione Edmund Mach ,5
European Space Agency
Biodiversity plays an important role in ecosystem
functioning by promoting a wide range of functions andservices. Functional diversity is a component of36

NDVI cannot grasp the variability of the functional
diversity.
Thus, the results obtained in this study show that theuse of sun-induced fluorescence can improve our ability
in functional diversity mapping compared to state of
the art measures based on vegetation indices orreflectance.

transpiration estimates do not. The ratio of bothtranspiration estimations therefore yields information
about the stress conditions. To test the validity of thecoupled model, we will perform a controlled field-scale
experiment. Here, the objective is to measure the SIF
using the FLoX instrument (JB Hyperspectral Devices,
Düsseldorf, Germany) as well as meteorologicalvariables (incident PAR, air temperature, wind speed,
atmospheric vapour pressure and air pressure),vegetation properties (biomass, LAI, stomatal
conductance, vegetation water content) and soil
moisture at different depths. Running the coupledmodel using the in-situ data will result in a ‘stress map’,in which the stress factor is calculated at field scale.
Comparing the measured data to UAV-based
multispectral data and pulse amplitude modulation(PAM) measurements will provide information about
the quality of the stress estimates.
References
Klosterhalfen, A., Herbst, M., Weihermüller, L., Graf, A.,
Schmidt, M., Stadler, A., Schneider, K., Subke, J. A.,
Huisman, J. A., Vereecken, H. (2017). Multi-site
calibration and validation of a net ecosystem carbon
exchange model for croplands. Ecological Modelling,363,
137–156.
https://doi.org/10.1016/j.ecolmodel.2017.07.028
Van Der Tol, C., Verhoef, W., Timmermans, J., Verhoef,A., & Su, Z. (2009). An integrated model of soil-canopy
spectral radiances, photosynthesis, fluorescence,
temperature and energy balance. Biogeosciences,
6(12), 3109–3129. https://doi.org/10.5194/bg-6-31092009

Field-scale monitoring of drought stress using
chlorophyll fluorescence with the coupled SCOPEAgroC model

De Canniere S1, Herbst M2, Defourny P1, Jonard F1,2

1
Uclouvain, 2Forschungszentrum Juelich
Field-scale monitoring of drought stress using
chlorophyll fluorescence with the coupled SCOPE-AgroC
model
Simon De Canniere1, Michael Herbst2, Pierre
Defourny1, François Jonard1,2
1Université catholique de Louvain, Earth and Life
Institute, Louvain-la-Neuve, Belgium
2Forschungszentrum Jülich GmbH, Institute of Bio- andGeosciences (IBG-3), Jülich, Germany
Keywords: sun-induced chlorophyll fluorescence,drought monitoring, field spectroscopy, radiativetransfer modelling, plant growth modelling
Droughts, which have become more frequent due toclimate change, cause social, economic and ecologicalharm. Sun-induced chlorophyll fluorescence (SIF) is apromising indicator for droughts, given its close link tophotosynthesis. This project is aims at developing amethodology to assess the effect of drought stress on
SIF emission, particularly in the period before damage
to the chlorophyll or plant structure has occurred.
Therefore, we propose a coupled model consisting of
SCOPE (van der Tol et al., 2009) and the plant growthmodel AgroC (Klosterhalfen et al., 2017). The SCOPE(Soil Canopy Observation, Photochemistry and Energy
fluxes) model is a radiative transfer model which can beused to simulate SIF based on optical and thermal
remote sensing observations above the canopy. AgroC
allows to model plant development at the field scale,i.e. the net ecosystem exchange (NEE) of carbon dioxide
and its two components, gross primary production(GPP) and ecosystem respiration (ER), consisting of an
aboveground and belowground part. The model makes
use of meteorological data, plant-specific parametersand soil characteristics. As photosynthesis is the main
driver behind both SIF and GPP, GPP can be retrieved
based on SIF. AgroC subsequently uses SIF based GPP
retrievals in order to improve its parametrisation. BothSCOPE and AgroC are capable of predicting oftranspiration. However, AgroC transpiration estimatesconsider possible drought stress, while SCOPE************************The effect of heat waves on the physiology and sun
induced fluorescence of citrus trees

Cochavi A1, Amer M1, Stern R1, Tatrinov F1, Schwartz E1,

Rotenberg E1, Yakir D1Earth and Planetary Science, Weizmann Institute Of
ScienceHeat waves (‘Hamsin’) are a common phenomenon in
the Mediterranean basin during springtime. It is
important to understand plant response to suchextreme events as their frequency and severity is
increasing with global climate change. Sun induced
fluorescence (SIF) offers a new means to detect canopy
scale chlorophyll fluorescence, as an intrinsic indicatorof changes in functioning of the photosynthetic
apparatus. It is measured in two specific wavelengths,
687 nm (SIF_B) and 760 nm (SIF_A). Previous reports
indicated correlation between ecosystem SIF_A andgross primary production (GPP). This suggests thatchlorophyll fluorescence is linked to electron transport
in the photochemistry pathway, but the effects of1

37

different environmental factors on this signal and its
relation to GPP is still unclear.
We studied the effect of 10 days seasonal heat wave ina citrus orchard in Israel from May to mid-June, whenthe maximum temperature ranged between 37-42ºC(compared with 23-28ºC in normal days), and vapor
pressure deficit (VPD) values were 3-8 KPa (comparedto 1-2 KPa in normal days). We used our mobile lab tocarry out eddy covariance measurements of water,
heat, CO2 and Carbonyl sulfide (COS) fluxes using aquantum cascade laser (QCL; QC-TILDAS-CS, Aerodyne
Research, Billerica, MA, USA) and Infra-red gas analyzer(IRGA; LI-7200, LI-COR, Lincoln, NE, USA). Continuous
SIF measurements were using a FloX system (JB
hyperspectral
devices,
Düsseldorf,
Germany).
Additional pulse amplitude modulated (PAM)
fluorescencemeasurements
were
conducted
periodically using Mini-PAM (Heinz Walz Gmbh,
Effeltrich, Germany).
During the study period, midday net ecosystem
exchange (NEE) and GPP decreased by ~50%. Midday
SIF_A signal decreased by similar values, compared tonormal days, but SIF_B signal, remained unaffected.
Comparing the daily patterns in SIF between normal
and heat wave days, demonstrated similar patterns
during the early morning and late afternoon hours,
while VPD values were low. However, during mid-day,
SIF_A signal decreased linearly with time during theheatwave, but remained steady during normal days.
Electron transport rate (ETR) measured with the miniPAM demonstrated similar patterns. In general, thedaily trend of SIF_A and the ETR was found to be highly
correlative (R2>0.8). The non-photochemical quenching(NPQ) values increased during the day with theincreasing VPD, during the heat wave. Uptake of COS,
sensitive to stomatal conductance, decreased during
the day, while VPD values increased during the heatwave.
The results demonstrated a correlation between SIF_A
signal and the electron transport rate. When stressconditions developed, plant stomatal conductancedecreased (decrease in the COS flux), reducing the CO2
uptake and, in turn, fixation. This was associated withincrease in NPQ probably to reduce over-excitationstress, while SIF_A decrease.
The results provide new insights to the effect of
extreme events on the SIF signal, and its physiologicalsignificance, which can help its applications in Ecophysiological studies of plant response to climatechange.

************************

38

the atmosphere column-averaged CO2 dry air mole
fraction (XCO2), recent studies have also demonstrated
that SIF can offer a new way for directly estimating theterrestrial gross primary production (GPP). The retrievalof solar-induced chlorophyll fluorescence on a global
scale will been made possible due to the high spectral
resolution measurements centered at 0.76 μm by the
TanSat–ACGS spectrometer with a spectral resolutionof 0.044 nm. Here, a micro spectral window (~ 2 nm)
covered Fe Fraunhofer line is used to explore thepotential of TanSat for solar-induced chlorophyll
fluorescence retrievals. The basic idea for this retrieval
in this work is distinguishing the in-filling effect ofFraunhofer line by fluorescence. The retrieval approachis based on the singular vector decomposition (SVD)
statistical method to derive the fluorescence-freecomponent in the solar radiance reflected by surfaceatmosphere. SVD is a method used to factor real orcomplex matrices. Similar to Principal Component
Analysis (PCA), it invelves the eigendecomposition of alarge set of observations of correlated variables into asmaller set of uncorrelated signals called singular
vectors. Normally, the singular value decomposition of
an m×n real or complex matrix. One year available
measurements are tested to produce the monthly
gridded averages on the global scale. Some otherremote sensing datasets are also used to validate thereliable of the fluorescence product derived in thiswork. An overall consistency of fluorescence intensity
and spatial patterns of TanSat with OCO-2 fluorescenceproduct on the global scale has been found in this work.
And the high agreement between TanSat fluorescence
retrievals and OCO-2 and other vegetation indices has
consolidated the confidence of the potential andfeasibility of TanSat fluorescence retrievals and opens
the applications of TanSat measurements in the futurescientific studies.
Keyword: TanSat; SIF; SVD; OCO-2; GPP
References:Frankenberg C, O'Dell C, Berry J, et al. Prospects forchlorophyll fluorescence remote sensing from theorbiting carbon observatory-2. Remote Sensing ofEnvironment, 2014, 147: 1-12.
Guanter L, Frankenberg C, Dudhia A, et al. Retrieval andglobal assessment of terrestrial chlorophyll
fluorescence from gosat space measurements. Remote
Sensing of Environment, 2012, 121: 236-251.

Posters

Is remotely sensed SIF providing information on SIF
yield?
Gentine P1, Zhang Y1, Pagan B2, Miralles D2
1Columbia University, 2University of Ghent
In order to evaluate the response of SIF yield to stressperiods due to heat waves or droughts, we here use amachine learning algorithm to retrieve SIF (normalized
by PAR) based on MODIS reflectance channels. The
retrieval should no direct physiological relationship tobiochemistry but we will demonstrate that it can stilllargely capture most stress periods. We will conclude
regarding stress impact on chlorophyll and canopy
structure.

************************

Global retrieval and assessment of terrestrial solarinduced chlorophyll fluorescence from TanSat
satellite measurements

Du S1

Institute Of Remote Sensing And Digital Earth, Chinese
Academy Of Sciences

1

The advent of the first Chinese carbon satellite, Chinese
Carbon Dioxide Observation Satellite Mission (TanSat,
also termed CarbonSat) launched on December 21,
2016, is the first Chinese satellite as an Earth
Observation project intended to the monitoring anddetection of atmospheric carbon dioxide (CO2). TanSat
flies in a sun-synchronous, 700 km altitude orbit with a
13:30 ascending local time and a revisit period of 16days. The Atmospheric Carbon dioxide Grating
Spectraradiometer (ACGS), which uses the grating
technique, is able to detect atmospheric O2 and CO2
absorption spectra in three narrow bands: near the O2A band, weak CO2 band and strong CO2 band. Although
the primary purpose of the TanSat mission is to retrieve************************

39

Comparing satellite observations and measurementsfrom the AtmoFLEX campaign using radiative transfer
calculations

allows simulating the spectral radiance at the bottom
and the top of the atmosphere. MOMO has been fed
with measurements gathered within the framework of
AtmoFLEX, AErosol RObotic NETwork (AERONET) dataand numerical weather prediction data by the HIRLAM
model. For the radiative transfer computations, abottom boundary condition is required. As spectrallyhigh resolved reflectances are available for the sites
from the Fluorescence boX (FloX) measurements, this isa suitable input to MOMO.
In order to validate the simulation approach, down
welling radiances as observed by FloX are simulated.
The simulation results of down welling radiances andthe measured down welling radiances have been
analyzed partially for the AtmoFLEX campaign.
Additionally, a comparison of FloX and multi-filter
rotating shadowband spectrometer (located at the
research center Jülich, Germany) down welling
irradiance will be presented.
The same atmospheric characterization can be used tosimulate space-borne measurements. Possible satellite
missions for comparing simulations and measurements
include Sentinel-3 and Sentinel-2. First simulation
results for satellite measurements are compared to therespective measurement. This approach can beextended to a longer time-series in order to getstatistically founded results.

Burba M1, Drusch M1, Schüttemeyer D1, Preusker R2,
Fischer J2, Julitta T3, Burkart A3, Bohn B4
1ESA/EOP, 2Free University Berlin, 3JB Hyperspectral,
4Forschungszentrum Jülich
Within the framework of the European Space Agency’s(ESA) AtmoFLEX campaign, fluorescence and collocatedatmospheric measurements have been collected tosupport the development of the fluorescence retrieval
algorithm for the FLuorescence EXplorer (FLEX) mission.
For this purpose, three instrumented sites in Europe
have been selected, which are located in Germany, Italy
and France. The sites locations cover different
ecosystems focusing on agricultural areas and forests.
Measurements at these sites address the scientificchallenges of the retrieval of fluorescence based onsatellite and airborne measurements. These sites
measurements include land surface properties likereflectance or vegetation type and cover as well as
atmospheric characterizations, namely aerosol load,type and height, humidity and temperature profiles.
The instruments provide continuous measurements
over months to generate statistically exploitable timeseries.
Point measurements of surface and atmosphericproperties are not necessarily representative for larger
spatial areas, for example a satellite sensor footprint.
The spatial resolution of FLEX is approximately 300m x
300m, thus using a point measurement to develop thefluorescence retrieval algorithm is only a starting point.
Within the framework of the ESA FLEXSense campaign,the HyPlant airborne sensor flew over the campaign
sites in order to map fluorescence during June/July
2018. In addition, the Ocean and Land Color Instrument(OLCI) on board of Copernicus Sentinel-3B was
reprogrammed for several acquisitions including the
campaign sites during its commissioning phase. The
reprogramming enabled OLCI to mimic the spectral
characteristics of FLEX in specific parts of theelectromagnetic spectrum. This three step scaling
approach,point
measurements–
airbornemeasurements – satellite measurements, will foster thedevelopment of the fluorescence retrieval algorithm
taking the influence of ecosystems, the weather andclimate zones into account. The combined
measurements are essential to validate and further
develop the atmospheric correction scheme for FLEX,
whilst the data may also be valuable for operational
missions like Sentinel-3.
The radiative transfer model MOMO solves theradiative transfer equation of the atmosphere-oceansystem using the Matrix Operator Method. MOMO************************
Method For Acquiring and Comparing Spatially
Explicit Measurements of Sun Induced Fluorescenceon the Ground
Emin D1, Matveeva M1, Acebron K1, Vierneisel B1,
Siegmann B1, Rademske P1, Burkart A3, Julitta T2
1
Forschungszentrum Jülich, 2University of MilanoBicocca, 3JB Hyperspectral
Sun-induced fluorescence (SIF) from plants is viewed
among the broader scientific community as a valuable
new source of information about plant functional
status. As a result of the increasing interest, new SIF
products derived from UAV, airborne, and spaceborne
sensors are becoming increasingly available. Validationof such remotely sensed SIF maps requires spatiallydistributed ground measurements of SIF taken at theexact time of sensor overpass. However, because
collecting spatially distributed SIF in larger areas is timeconsuming, the majority of observations will be awayfrom the exact time of overpass. Here, an outline for anempirical approach is proposed which corrects for the
diurnal cycle and recalculate SIF for any given momentin time. The approach requires one single observationof SIF for the location of interest at any time, a diurnal
SIF curve for the crop type (modeled or measured), and40

an estimate of the amount of biomass at the location ofinterest and the location of diurnal SIF measurement.
To prove the feasibility of the method, we conducted aspatially distributed measurement of SIF in two crop
fields modifying an existing hyperspectral point
spectrometer (D-FLOX) for mobile use. Leaf area index(LAI), leaf chlorophyll content, plant height, and otherrelevant biophysical parameters were also recorded ateach location. Alongside the mobile SIF sampling effort,
an identical and intercalibrated device was installed ona permanent position to record the diurnal SIF cycle.
Spatially distributed SIF from 46 locations (15 in sugar
beet and 31 in winter wheat) collected on three
separate dates between the hours of 10:00 and 14:00
were recalculated to solar noon using the proposedcorrection scheme and both raw and corrected SIF
values were compared to LAI. We observed a better
correlation and linear model performance against LAI
for diurnal cycle corrected SIF. The locations in sugar
beet were measured at the time of a low altitude
overpass of the airborne hyperspectral sensor designed
for SIF retrieval (HyPlant). Therefore, in a second step,
SIF estimates in sugar beet were recalculated to theexact time of overpass and compared against the
HyPlant derived SIF maps. In summary, a spatially
explicit SIF sampling measurement protocol and simple
empirical approach to correct for the distinct diurnal
cycle of SIF are proposed. Such measurement approach
can be used to study the spatial heterogeneity of SIF in
small areas, to measure a large number of plots in field
phenotyping set-ups, or to recalculate SIF in physicalunits for any given time of the day, e.g. for validation of
airborne data.

future. To monitor the temporal changes in ecosystem
function, Earth-observation satellite is a powerful tool.
In recent years, satellite observed Solar Induced
Fluorescence (SIF) is used to obtain the photosynthetic
production or environmental stress for plants. The
temporal changes in the satellite-based SIF would begood index to evaluate the ecosystem services.
By using temporal and spatial changes in SIF observed
GOSAT, GOME-2, and OCO-2, we are trying to map thevalue of the ecosystem service in South-East Asia. Since
these satellites have different spatial and time
resolution, using multiple satellite data enable us to findextreme climate events easily. On the other hand, we
have to consider the difference in observation time;GOME-2 observes in the morning whereas GOSAT and
OCO-2 observe at midday. In this presentation, first, we
will show the temporal variations of SIF in South-East
Asia. In addition, we will show the map of ecosystems
with strong resilience.

************************LASVEG: a combined airborne instrumental platform
for simultaneous measurements of laser-induced
fluorescence, SIF, visible reflectance and verticalstructure of the canopy
Ounis A1, Salvador H1, Bousquet O1, Kamal El Idrissi H1,
Moya I1, Goulas Y1
Dynamic Meteorology Laboratory
The forthcoming FLEX mission of ESA will provide new
fluorescence products, including the two chlorophyll
fluorescence peaks in the red and far red, atunprecedented spatial and time resolution. New
insights on the ecophysiological processes of vegetation
at large scales are expected, linked to climate andenvironmental conditions changes. Chlorophyll
fluorescence (ChlF) is tightly linked to photosynthetic
processes as it competes with the other deactivation
pathways of the absorbed energy, namely
photochemical conversion and heat dissipation. Indeed,
ChlF is routinely used at leaf level to quantify
photosynthesis using active techniques. However,when using passive techniques, the link between suninduced fluorescence (SIF) and photosynthesis still need
to be clarified across spatial (leaf, canopy, ecosystem,
regional, global) and temporal (hours, season, years)
scales. We propose here a new airborne instrumental
platform (LASVEG) that combines active and passive
measurements of ChlF. Additionally, LASVEG will
monitor the vertical structure of the canopy by laser
waveform analysis. Laser-induced fluorescence (LIF)
will provide a direct assessment of fluorescencequenchings at the canopy scale, offering a validation1************************The evaluation of ecosystem service by satellitebased SIF in South-East Asia

Murakami K1, Saito M1, Noda H1, Oshio H1, Yoshida Y1,

Matsunaga T1
National Institute for Environmental Studies
Primary production of terrestrial ecosystems supports
all ecosystem services. Since climate conditions affectphotosynthetic activity directly, recent global warming
may damage or enhance the primary production of theecosystem. Even if some extreme climate event
damages the ecosystem, it would be recover and theresilience is important for the ecosystem service. The
ecosystem resilience shows remarkable spatial
variation because it depends on various environmental
factors, including meteorological aspects and species
composition of plants. Thus, to monitor the temporal
trends in primary production enable us to identify thevaluable ecosystem under climate changes in near1

41

tool for fluorescence models and space data processing
at the landscape and regional scale. LASVEG will be
integrated on the research aircraft ATR42 from the
French institution Safire. We present here the maintechnical features of LASVEG, as well as recent
developments and first tests results.

from 0° to 315° in steps of 45°. These repeatable cycles
were sampled continuously during a day from 9 am to 6
pm to characterize F and PRI anisotropy at different
times of the day. In addition, canopy height, LAI andchlorophyll content were collected in the field, alongwith images for 3D canopy reconstruction.
The results showed, that multi-angular F760 and F687
of homogenous fully developed canopies have a distinct
dome-like shape in the solar principal plane, with the
maximum values occurring in the hotspot direction andminimum values in the forward scatter direction. In
contrast, multi-angular F760 and F687 of row crops
show a more complex hemispherical distribution.
Overall, we observed strong positive correlation
between F and HCRF at the corresponding wavelength(F760/R750 and F687/R680) in the solar principal plane,
which was stable during the whole day.
Opposite to F variations, PRI exhibited strong
directional responses for all homogeneous canopies
with the highest values retrieved at VZAs corresponding
to the forward scatter direction, and the lowest at the
hotspot in solar principal plane, which can be explainedby PRI sensitivity to sunlit and shaded canopy fraction.
The effects of sun-view geometry and LAI and LIDF
parameters on spectro-directional F and PRI outputs
were tested with the SCOPE model and compared withfield observations. The obtained dataset of multiangular F and PRI of five canopy types considerably
contributes to our understanding of the anisotropic
behavior of the signals.

************************
Characterization of sun-induced fluorescence and PRI
anisotropy based on field spectroscopy data

Biriukova K1, Celesti M1, Evdokimov A1, Panigada C1,

Anelli M1, Tagliabue G1, Julitta T2, Boschetti M3,
Migliavacca M4, Colombo R1, Miglietta F5,
Schüttemeyer D6, Rossini M1
1
University Of Milano-Bicocca, 2JB Hyperspectral
Devices UG, 3Institute for Electromagnetic Sensing of
the Environment (IREA-CNR), 4Max Planck Institute for
Biogeochemistry, 5Institute of Biometeorology,
National Research Council (IBIMET-CNR), 6European
Space Agency,ESTEC
Recent studies have shown that sun-induced
fluorescence (F) and Photochemical Reflectance Index(PRI) are characterized by noticeable directionalvariations, controlled by leaf and canopy structure (LAI,
gap fraction and leaf inclination distribution - LIDF),
pigments presence and sun-observation geometry that
influence the light distribution, scattering andabsorption inside the leaf and the canopy. Although inprevious studies F and PRI were used for monitoring thephotosynthetic activity, their anisotropic behavior was
not yet fully characterized. An improved understandingof these directional variations can potentially help todisentangle directional from physiological responses in
the continuous long-term optical measurements as wellas to improve anisotropy correction models for
airborne and spaceborne data. Therefore, the aim of
this research is to contribute to the understanding of F
and PRI directionality based on the field spectroscopy
data.
The canopy bi-directional spectra were acquired with
the FloX system (JB Hyperspectral Devices UG),
specifically designed to measure F760 and F687 andvisible-near infrared radiance. The FloX was coupledwith a goniometer device, allowing to vary view zenith
angles (VZA) and view azimuth angles (VAA). We
collected multi-angular datasets of F andhemispherical–conical reflectance factor (HCRF) in
Mediterranean tree-grass ecosystem over theherbaceous stratum in Las Majadas de Tiétar, Spain andover alfalfa, chickpea, corn and rice crops in Braccagni,
Italy. Spectral measurements were acquired with a fieldof view of 25°. The view zenith angle varied from 0° to
45° in steps of 15° while the view azimuth angle varied************************
Quantitative assessment of Sun-InducedFluorescence maps from HyPlant airborne images
using different quality criteria - Part II

Krieger V1, Siegmann B1, Matveeva M1, Rademske P1,Heid P1, Gruenhagen L1, Muller O1, Cogliati S2, Damm
A3, Rascher U1
1
Institute of Bio- and Geosciences, IBG-2: Plant
Sciences, Forschungszentrum Jülich GmbH, 2Remote
Sensing of Environmental Dynamics Lab., DISAT,
University of Milano-Bicocca, 3Department ofGeography, University of Zurich
The ability to investigate the Earth’s environment will
be largely improved by hyperspectral satellite data. The
FLuorescence EXplorer (FLEX) will be the first
hyperspectral mission designed to monitor thephotosynthetic activity of the terrestrial vegetation
layer by using a completely novel technique measuring
the sun-induced chlorophyll fluorescence (SIF) signalthat originates from the core of the photosynthetic
machinery. In preparation of the upcoming FLEX
satellite mission that will be launched in 2022, a large

42agriculture landscapefield campaign, namely FLEXSense, was conducted insummer 2018 including representative study sites atseveral locations in middle and south Europe as well asNorth America.
During the various field activities, airborne data was
acquired with the hyperspectral airborne imager
HyPlant that consists of two sensor heads. The DUAL
module is a line-imaging push-broom sensor providing
contiguous spectral information from 380 to 2500 nm.
The FLUO module measures radiance in high spectral
resolution (0.25 nm) in the spectral region of the twooxygen absorption bands covering a range from 670 to
780 nm and facilitates a reliable retrieval of thechlorophyll fluorescence signal. Currently, two different
algorithms are routinely used to retrieve red (SIF680)
and far-red SIF (SIF760) from HyPlant data. Bothmethods exploit oxygen absorption bands for the
retrieval. While the improved Fraunhofer Line Depth(iFLD) approach employs a semi-empirical atmosphericcorrection (i.e. using bare soils), the Spectral Fitting
method (SFM) is coupled with a physically-based
atmospheric correction (MODTRAN5 code).
A common method of testing the reliability of remotelysensed SIF (in this study airborne maps) is thecomparison with “ground truth” data. In many cases,
however, ground measurements of SIF are not available
or are too labor-intensive to be measured at regional
level. For this reason, we developed an alternative
approach based on image based quality criteria toassess the quality of airborne SIF maps. The set of
quality criteria (e.g. signal-to-noise ratio, correlation
with vegetation indices, plausibility checks, etc.) helps
identifying and quantifying errors and artifacts inretrieved SIF maps.
In this contribution, we outline the defined set of
quality criteria and demonstrate their capability todetermine the quality of individual SIF maps derived
from HyPlant images acquired during the 2018
FLEXSense campaign. The application of the proposed
quality features proved to be a valuable tool forassessing the quality of SIF maps derived from HyPlant
airborne data. We suggest to apply this set of criteria in
addition to validation attempts that employ groundreference measurements. This allows providing
complementary information about the SIF retrieval
accuracy and the quality of entire SIF maps.

Matveeva M1, von Hebel C2, Marke T3, Rademske P1,Emin D1, Krieger V1, Damm A4, Cogliati S5, Brogi C2,
Waldhoff G6, Lussem U6, van der Kruk J2, Crewell S3,
Rascher U1
1
Plant Sciences (IBG-2), Institute of Bio- andGeoscience, Forschungszentrum Jülich, 2Agrosphere(IBG-3), Institute of Bio- and Geoscience,
Forschungszentrum Jülich, 3Institute for Geophysics
and Meteorology, University of Cologne, 4Remote
Sensing Laboratories, University of Zurich, 5Remote
Sensing of Environmental Dynamic Lab., University of
Milano-Bicocca , 6Institute of Geography, GIS & RS,
University of Cologne
There are strong interactions between soil properties,
plant growth and atmosphere. We use sun-induced
Fluorescence (F) of vegetation to obtain remotely
information about the plant physiological status thatcan be linked to soil and atmospheric properties,
improving our understanding of energy and matter
flows. F is a signal closely related to the actual rate ofphotosynthesis and vegetation stress. It reflects
functional limitations of the photosynthetic carbon gain
and can be measured remotely in solar andatmospheric absorption lines using high performance
spectrometers. The future satellite mission of The
FLuorescence EXplorer (FLEX) will allow for the firsttime monitoring of F over the globe providing thehyperspectral data with required resolution.
During several years we have collected data for spatial
analyses using the high performance imaging
spectrometer HyPlant, measuring in wavelength ranges
380 – 970 nm with resolution 4.2 nm, 970 – 2500 nm
with resolution 13.5 nm and 670 – 780 nm with highspectral resolution of 0.26 nm. The HyPlant data were
processed using iFLD (Improved Fraunhofer Line
Discrimination) and SFM (Spectral Fitting Method).
Data were recorded on a ca. 14x14 km2 area around
Forschungszentrum Juelich (Germany) with a spatial
resolution of 3 m per pixel. Land cover of this region isclassified mostly as crop fields, some mixed forest
patches and some residential/industrial areas. Also two
pit mining zones are presented in the scene. Within thislarge area, another specific area used mostly for crop
production and with a size of ca. 1.5×5 km2 near a townof Selhausen was chosen to acquire data with 1 m
resolution. Selhausen area was better characterized interms of land use classification, soil properties andground measurements of F and reflectance by
FloxBoxes. Furthermore, an Eddy Covariance (EC) tower
was present in this area.
We have analyzed data collected by HyPlant in thefootprint of a scanning passive microwave radiometer(MWR) measuring integrated water vapor (IWV). This************************
Linking spatial Fluorescence patterns to soil andatmospheric properties in a heterogeneous

43

allows us to link the plant functioning to the regional
atmospheric water vapor patterns. For this purpose wehave used F and common vegetation indices bycomparing them to values of IWV for all azimuth
directions measured during the time of the HyPlant
overflight above the region of interest.
Recently, different crops were investigated and it was
shown that the within-field heterogeneity of F causedby differences in plant performance is related to
specific subsurface structures identified by quantitative
multi-coil electromagnetic induction (EMI) data
inversions. The inverted electrical conductivity of theploughing layer showed minor correlation to
fluorescence data, while the correlation between thesubsoil conductivity and far-red fluorescence indicate asignificant influence of the subsoil on plant
performance, especially during dry periods. Moreover,distinct F patterns were created by differences in waterholding capacity of soil at depths of 1 m and deeper,
which means that F data can contain soil moisture
information at depth. Together with quantitative EMI
data inversions, this information can be used to reduce
existing uncertainties in assessing the efficiency withwhich plants access and use the soil water/nutrient
resources.

conventional WUE parametrization, a nearly-linear
function of atmospheric CO2 partial pressure, fails toaccount for the information content of plant stomatal
configuration in response to other emerging
environmental controls (such as soil moisture, plant
hydraulics and/or vapor pressure deficit). This is ofparticular importance for the understanding andpredictability of water and carbon cycles under current
and future climate change scenarios, where theconventional assumption of a linear (one-to-one)correlation between A and T would tend to propagate
relatively large errors and uncertainties into model
estimates of T informed by A and WUE. Capitalizing on
recent progress made in mechanistic modeling of leaflevel gas exchange processes, this study aims to provide
an improved representation of physical mechanisms
constraining WUE. The new parametrization explicitly
accounts for the stomatal response to environmental
changes reflected in a varying intercellular CO2
concentration (as opposed to the traditional
assumption of a constant value). Given the difficulties
in quantifying intercellular CO2 concentration dynamics
at operational scales, we propose a theoretical solutionin which the supply of CO2 via the stomata (A) andbiochemical demand for CO2 are constrained by thebalance between loss of water vapor from the leaf tothe atmosphere (T) and supply of water from soil to theleaf through the soil-root-xylem system. We test themodel estimates of A and T using field observations in amixed forest and cropland, and discuss its potential
benefits to expand the utility of remotely sensed
photosynthetic (A) proxies, such as SIF, into estimationof ecosystem T and prediction of carbon-water relations
in a changing environment.

The extensive dataset collected and processed during
the last years allows us to perform detailed analyses ofinteractions within the soil-plant-atmosphere system.
The aim of this work is inclusion of such interactions
into soil-plant-atmosphere models for root water
uptake and evapotranspiration processes as well as into
harvest predictability tools.

************************************************
Canopy architectural influence on the interpretationof the biophysical parameters and sun-induced
chlorophyll fluorescence variability: A small-scalelaboratory experiment.

Mechanistic modeling of leaf gas exchanges expands
the utility of SIF into estimation of ecosystemtranspiration

Haghighi E1, Paul-Limoges E2, Damm A1,2

Moncholi A1, Alonso L1, Van Wittenberghe S1, Cendrero-

Swiss Federal Institute of Aquatic Science andTechnology, 2Department of Geography, University of
ZurichPlant gas exchange through leaf stomata plays a criticalrole in terrestrial water and carbon cycles, regulating
the trade-off between photosynthetic carbon gain (A)and transpirative water loss (T). This is often
characterized by plant water use efficiency (WUE – theratio of A to T), a critical ecosystem indicator for how
plants have adapted (or will adapt) to the physicallimitations of their changing environment. Given thatthe diffusive fluxes of A and T across stomatal pores arelinearly proportional to stomatal conductance, the1Mateo M1, Malenovský Z2,3, Moreno J1
1
University of Valencia, 2Geography and Spatial
Sciences, School of Technology, Environments andDesign, University of Tasmania , 3Global Change
Research Institute CAS
Within preparation of the upcoming FLuorescence
EXplorer (FLEX) satellite mission, several chlorophyll
Sun Induced Fluorescence (SIF) studies induced asignificant knowledge on vegetation physiological andphotosynthetic dynamics. To understand thesecomplex dynamics, biophysical parameters related tolight use efficiency, concentration of foliage pigments44

or leaf photochemical status are required tocomplement the information provided by SIF. Although
all these parameters need an accurate estimation of the
at-target incoming radiance, the most extended
approach is to use the top of the canopy incoming
radiance, while neglecting the vegetation structural
heterogeneity. Therefore, it is necessary to investigate
the impact of the canopy structure on radiance-derived
measurements.
The main objective of this work is to study the effect ofthe vegetation architecture, i.e. foliage geometry andclumping, on spectroscopic estimation of vegetation
biophysical parameters crucial in SIF studies. This study
shows the variability and differences between
measurements of the top of canopy radiance obtained
from a horizontal white reference panel and as
measured at the surface of photosynthetically active
leaves. Additionally, it demonstrates, on few examples,the canopy structural influence on quantitative
estimations of vegetation indices related tophotosynthetic processes, such as an incoming leaf
photosynthetic active radiation (PAR), chlorophyll
content (approximated by MTCI), and photoprotection
status (approximated by PRI).
In this study, crowns of healthy beech saplings (Fagus
sylvatica L.) were measured in laboratory under stableenvironmental and illumination conditions. Top-ofcanopy spectral measurements were performed with apush broom system, which consists of a HySpec VNIR
scanner (Photon Systems Instruments, around 1 nm
spectral resolution and 350-900 nm spectral range) anda halogen lamp. Small white Spectralon reference
panels (1 cm2) were attached to several leaves withvarying orientation angles at different depths of the
canopy vertical profile. Additionally, a larger whitereference panel was allocated horizontally next to theplant, perpendicular to the sensor optical plane,
covering the entire field of view of the instrument andproviding the top-of-canopy radiance.
This work is aiming at development of new methods forcorrecting the canopy structural influence in the remotesensing measurements of vegetation physiological state
traits, in support of the development of high-level FLEX
products.

Field spectroradiometric measurements as well as
imaging spectroscopy study the interrelationships
between the spectral characteristics of objects andtheir biophysical attributes in the field environment.
With the advancements in sensor technology also finer
spectral features can be measured by these
instruments.
One example is sun-induced fluorescence (F).
Still, measuring and interpreting the F signal remains
challenging, both regarding the post-processing and F
retrieval step with factors driving the offset between
the emitted versus the retrieved F signal, and the Finterpretation step, with factors related to the
dynamical physiological behaviour of vegetation and its
structural effects. The first step includes factors related
to the instrumental responses, specifications and theplatform/measurement set-up.
To meet these challenges, many researchers haveworked within the framework of an european
cooperation in science and technology (COST) action
ES1309 to develope innovative optical tools forproximal sensing of ecophysiological processes(OPTIMISE). To make this information available, the
OPTIMISE community has compiled three papers on
instrument characterisation, measurement setups andprotocols and retrieval techniques. These reviews aim
summarize the state-of-the-art for highly precise
radiance measurements with focus on F to pursue thealmost 10 years old review paper of (Meroni et al.,2009).
With this poster we would like to present the main
outcomes on the measurement setups and protocols
used to measure F at the leaf to canopy scale, including
the discussion on important metadata to capture alongwith the measurements.

************************
Temporal upscaling solar-induced chlorophyll
fluorescence from the instantaneous to continuous
scale causes an improved correlation with grossprimary productivity

Hu J1,2, Liu L1************************Key Laboratory of Digital Earth Science, Institute ofRemote Sensing and Digital Earth, Chinese Academy of
Sciences, 2University of Chinese Academy of Sciences
Solar-induced chlorophyll fluorescence (SIF) is closely
linked to the photosynthesis of plants and has thepotential to estimate gross primary production (GPP) at
different temporal and spatial scales. However,remotely sensed SIF at ground or space level is usually
instantaneous, which cannot represent the daily total
SIF. The temporal mismatch between instantaneous SIF
1Measuring sun-induced fluorescence at different
scales: Overview over instruments, measurement
setups, protocols and their application at leaf andcanopy scale

Aasen H1, OPTIMISE community
ETH Zurich

1

45

(SIFinst) and daily GPP (GPPdaily) impacts theircorrelation across space and time. Previous studies
have upscaled SIFinst to the daily scale based on thediurnal cycle in the cosine of the solar zenith angle(cos⁡(SZA)) to correct the effects of latitude and lengthof day on the variations in the SIF-GPP correlation.
However, the important effects of diurnal weatherchanges due to cloud and atmospheric scattering were
not considered. In this study, we presented an SIF
upscaling method using photosynthetically active
radiation (PAR) as a driving variable. First, a conversion
factor (i.e., the ratio of the instantaneous PAR (PARinst)
to daily PAR (PARdaily)) was used to upscale in-situ SIF
measurements from the instantaneous to daily scale.
Then, the performance of the SIF upscaling method wasevaluated under changing weather conditions anddifferent latitudes using continuous tower-based
measurements at two sites. The results prove that our
PAR-based method can reduce not only the latitudedependent but also the weather-dependent variationsin the SIF-GPP model. Specifically, the PAR-based
method gives a more accurate prediction of diurnal anddaily SIF (SIFdaily) than the cos⁡(SZA)-based method,with decreased relative root mean square error(RRMSE) values from 42.2% to 25.6% at half-hourintervals and from 25.4% to 13.3% at daily intervals.
Moreover, the PAR-based upscaled SIFdaily had astronger correlation with the daily absorbed PAR(APAR) than both the SIFinst and cos⁡(SZA)-based
upscaled SIFdaily, especially for cloudy days with acoefficient of determination (R2) that increased fromapproximately 0.5 to 0.8. Finally, the PAR-based SIFdaily
was linked to GPPdaily and compared to the SIFinst orcos⁡(SZA)-based SIFdaily. The results indicate that the
SIF-GPP correlation can obviously be improved, with anincreased R2 from approximately 0.65 to 0.75. Our
study confirms the importance of upscaling SIF from theinstantaneous to daily scale when linking SIF with GPP
and emphasizes the need to take diurnal weatherchanges into account for SIF temporal upscaling.

at a mature Eucalypt forest site – Tumbarumba(Australia). The Tumbarumba site is a member of
FLUXNET, SpecNet, and a CEOS Land Product Validation(LPV) SuperSite.
High-resolution multi-angular imagery of tree crowns is
acquired by the Headwall VNIR N-series line scanner,enabling vegetation and non-vegetation classification,in addition to sunlit and shaded pixel separation.
Radiance is measured in the 400-800 nm range (538wavelength bins), coincident with hemispherical
irradiance measurements for computation of areflectance factor. Consequently, the monitoring system
has been used to characterise the significant sun andsensor geometry effects at both diurnal and seasonal
time scales.
Our recent work has characterized the seasonal effects
on the PRI signal, likely caused by changing pigment
concentrations. Similar to other vegetation types wefound the seasonal constitutive changes in PRI faroutweighed the dynamic facultative changes at thedaily to weekly time-step. This finding was further
corroborated by field sampling, controlling for lighting
and structure, where the natural constitutive variation
among trees and within crowns was greater thanfacultative PRI changes varying in response to direct anddiffuse lighting conditions. Results characterizing
canopy BRDF from the proximal sensing system will bepresented alongside relationships between corrected
spectral indices and flux tower GPP. The importance oflinking leaf-level measurements with site-scale proximal
measurements is emphasized.

************************
Return of experience from the Sentinel-3 Tandem andlessons learned for FLEX

Clerc S1, Lamquin N1, Bourg L1, Henocq C1, Blanot L1

Acri-stDuring its commissioning phase, Sentinel-3B was flying
in close formation (30 seconds) with Sentinel-3A. This
presentation will highlight some of the lessons learned
from this tandem phase that can be applied to the
future FLEX-Sentinel-3 tandem.
1************************
Separating physiological from sun-view geometryeffects with a high resolution proximal hyperspectral
imager on the Tumbarumba forest flux tower

First, the tandem phase has proved extremely useful for
supporting commissioning operations, including
validation of performances and investigation of
anomalies. The tandem configuration allows intersensor validation with an unprecedented level ofaccuracy, and provides a unique opportunity to quantify
uncertainties on products. For FLEX and Sentinel-3, thismeans that a very fine inter-calibration of the sensors

Woodgate W , Suarez L , van Gorsel E , Hughes D ,Held A1
1
CSIRO, 2ANU, 3The University of Melbourne,
4
Independent
To better link dynamic canopy physiology to the spectral
signal we developed a fully automated hyperspectral
and thermal monitoring system installed on a flux tower
1

3

4

2

46

will be most probably reachable, which will benefit not
only FLEX but also the Sentinel-3 optical mission andvegetation products. As an illustration, we will show
how uncertainties on OGVI products can be assessedthanks to tandem data.

Although the GPP – SIF relationship has been
investigated at multiple scales, little is known about SIF
dynamics at ecosystem level and its links with GPP andtranspiration (T). Consequently, the understanding of
the mechanistic relationship between SIF GPP and T islimited. Recently, there is evidence that suggests thatSIF could be a reliable tool to monitor not only GPP, butalso T, as T is mediated by stomatal conductance andtypically tightly coupled with photosynthesis.

To fully benefit from the tandem phase, we have shownthat all known instrument differences shall be carefully
considered. In particular, fine spectral response
function differences have to be accounted before
comparing the measurements. This concerns
differences not only between instruments but also
within the field of view. To this respect, the fact that theswath of FLEX will remain within the swath of a single
OLCI camera is critically important.

As new instruments for proximal remote sensing of SIF
are being developed, collecting time series of SIF withhigh temporal frequencies at flux tower locations is now
operational. Additionally, modelling of SIF emission andtransfer within the canopy has become increasingly
accurate as models such as the radiative transfer andenergy balance model SCOPE (soil canopy
photosynthesis and energy) are being validated at
different ecosystems.

A third outcome of the tandem phase is the possibility
to assess the impact of the formation time lag on theobservation conditions, (in particular cloud motion andviewing geometry). At the end of the tandem phase,
Sentinel-3B has been manoeuvred to drift slowly awayfrom Sentinel-3A. It is therefore possible to analyse
quantitatively the impact of the time difference on themeasurements. Effects of cloud motion is apparent
even at short time scales (30 s) but has been shown tobe relatively easy to handle. In fact, the very fact thatclouds are moving or evolving make them easy to detectand discriminate from other bright objects. The impactof viewing conditions on TOA observation starts
becoming important only for larger time differences,
except on very reflective surfaces (sun glint). These
results indicate that a 30-second formation could be
sufficient to meet FLEX observation requirements.

Time series of SIF are characterized by high temporalfrequency and when paired with time series of T
derived from sap flow or from partitioning eddy
covariance evapotranspiration, and GPP derived fromeddy covariance, they can open new perspectives tounderstand the degree of temporal variability in GPP, T
and SIF that occurs at the ecosystem level.
In this contribution we make use of data collected at the
research site Majadas de Tietar, a tree grass ecosystemequipped with multiple ecosystem and sub-canopy
eddy covariance towers and a Fluorescence BOX (FLOX,JB Hyperspectral Devices, Düsseldorf, Germany) thatcollects at high temporal resolution Hyperspectral
measurements for SIF retrieval. Our objective is toevaluate the relationship between GPP, T and theecosystem scale water use efficiency (WUE) with SIF.

************************
Time series of Sun-Induced Fluorescence, Gross
Primary productivity and Transpiration in a
Mediterranean grassland

Making use of both data-driven techniques and the
SCOPE model, we aim to investigate the degree of
coupling between GPP, T, WUE and SIF at different
time-scales as well as the relationships between thefluxes and SIF. SCOPE model runs forward based on
observations of model parameters to understand thefactors controlling the relationship between
transpiration-WUE-GPP-SIF from daily and seasonal
time scale. Preliminary results will be shown in thiscontribution.

Martini D1, Pacheco-Labrador J1, El Madany T1, van der

Tol C , Julitta T , Burkart A , Biriukoa K , Rossini M ,Carrara A5, Migliavacca M1
1
Max Planck Institute For Biogeochemistry, 2Twente
University, 3JB hyperspectral devices, 4University of
Milano Bicocca, 5Centro de Estudios Ambientales delMediterráneo
Sun induced fluorescence (SIF), the radiation flux
emitted by plant chlorophylls molecules in the 650-800
nm spectral window, is considered an indicator ofphotosynthetic performance. Recently it has beenshown that SIF can track changes in light use efficiency(LUE), and therefore it is a good predictor of grossprimary production (GPP) at various scales, from leaves
and ecosystem to regional and global scale.
2

3

3

4

4

************************

47

Phenological changes in GOSAT SIF in temperate
vegetations in Japanbackground is naturally subjected to rapid changes in
response to light, temperature and/or stress. To
overcome such limitation, the idea was explored tocreate an "artificial fluorescing target" by incorporating
fluorescent dyes on an artificial coating mimicking thereflectance response of the vegetation. This type of
coating is well known especially in military applications
for the "camouflage" of sensible targets on the ground.
This poster illustrates the preliminary results of theincorporation of fluoresceing dyes in a camouflage
background and illustrates the reflection spectra which
may be obtained as well as the SIF retrieval. Potential
applications of this type of artificial targets for thecalibration of ground and airborne SIF sensors as well as
for the validation of atmospheric correction schemes isfinally discussed.

Noda H1, Yoshida Y1, Oshio H1, Matsunaga T1

National Institute For Environmental Studies
In temperate region, leaf phenology, including thetiming of onset and offset of leaves and temporalchanges in ecophysiological parameters of single leaf
determine the annual carbon gain of the vegetation.
Since the leaf growth and senescence are depend on
temperature condition, climate change might strongly
affect the phenological pattern. Thus, to find the effectof climate change on the vegetation, it is effective tomonitor the leaf phenology. Satellite remote sensing isuseful tool to monitor the temporal and spatial
variations in the structure and physiological traits ofcanopy. Previous studies have shown that satelliteobserved vegetation indices, such as NDVI and EVI areavailable to detect leaf onset and offset. However, it isdifficult to monitor leaf growth and senescence bysatellite observation because those indices indicate
only amount of leaves in the canopy. In recent years,
solar-induced chlorophyll fluorescence (SIF) has
observed by satellite such as GOSAT, GOME-2 and OCO2. GOSAT-2, launched on 29th October 2018 will also
observe SIF. Since SIF linked with photosynthetic
activity itself, it might be suitable index for leaf
phenology. In present study, we focused on three areas
with different vegetation types and temperature
conditions in Japan and showed temporal changes in SIF
observed by GOSAT in those area. Those three areas
showed different seasonal pattern in SIF. We will
discuss main cause of the phenology in SIF in temperateregion and availability of GOSAT and GOSAT-2 SIF as anindicator of leaf phenology.
1************************
Validation of atmospheric correction: Collaborationand exchange between Copernicus Sentinel-2 andSentintel-3 teams?

Pflug B1, Main-Knorn M1, de los Reyes R2, Louis J3,

Boccia V4
1
DLR - German Aerospace Center, 2DLR - German
Aerospace Center, 3Telespazio France – A Leonardo /Thales Company, 4ESA/ESRINThe Copernicus programme is a European initiative forthe implementation of information services dealing
with environment and security, mainly based on
observation data received from Earth Observation
satellites. In the frame of this programme, ESA launched
the Copernicus Sentinel-2 and Sentinel-3 opticalimaging satellites and is preparing the FLEX-Explorer
mission. These satellites deliver a new generation of
optical data products designed to directly feed
downstream services mainly related to land monitoring,
emergency management and security. Synergistic data
analysis involving FLEX, Sentinel-3 and Sentinel-2
missions is an upcoming topic which combines andexploits the spatial and spectral benefits of each ofthese missions. However, this can only be successful if
the uncertainties in the data to be combined are known
and reported in a similar way.

************************
Towards field-deployable fluorescing reference
targets

Miglietta F1, Armaroli N2, Barbieri A2, Genesio L1

IBIMET-CNR (Inst. of Biometeorology), 2ISOF-CNR (Inst.
of Organic Synthesis and Photoreactivity)
The retrieval of solar induced fluorescence (SIF) fromplants and canopies makes use of specific schemes
using either Fraunhofer or Oxygen-absorption bands.
Proper calibration of the retrieval schemes isproblematic as the fluorescence signal of Chlorophyll
adds to a background having peculiar reflectanceproperties, such as that of the vegetation. The idea ofartificially adding known amounts of light in the
fluorescence bands to a naturally fluorescing
background (vegetated surface) is certainly aninteresting option for calibration, even if the fluorescing
1

Atmospheric correction of satellite observations is aprecondition for most higher-level applications.
Development of atmospheric correction processors
includes their validation, which provides performanceof the algorithm and uncertainty of resulting products.
Even if different atmospheric correction algorithms aredeveloped and used for Sentinel-2 and Sentinel-3 data48

and are being developed for FLEX-mission, there is ahigh synergy potential regarding validation.

Scots pine canopy at the Hyytiälä Forestry Field Stationin Finland. A Monitoring PAM was mounted within the
canopy adjacent to the footprint sampled by the opticalsystem. Following correction of the SIF data for O2 andstructural effects, SIF, LUE, PRI and NDVI exhibited a
distinct seasonal pattern that followed GPP sampled by
the eddy covariance system. Due to the complexities ofsolar azimuth and zenith angle over the season on the
SIF signal, correlations between SIF, SIF yield, GPP and
LUE were restricted to SZA<50o, under strictly clear sky
conditions which resulted in only modest correlations(~r2=0.3). The diurnal responses of SIF, SIF yield andPAM parameters (F/Fm’) and meteorologicalparameters demonstrated improved agreement overthe diurnal cycle. This study found that optical samplingat this fine spectral, spatial and temporal resolution, theretrieved SIF signals did not perform well without astructural correction, and even then heavy filtering of
the data was required to include only the highest SZAand SAA conditions which resulted in convincing
relationships with GPP and LUE

The presentation demonstrates the current validation
methodology for atmospheric correction of Sentinel-2
data. Aerosol optical thickness and water vapour
outputs of atmospheric correction algorithms Sen2Cor
and PACO can be directly compared with reference data
available from AERONET sunphotometers. Performance
analysis of surface reflectance (SR) is done bycomparison of processor outputs with so called
AERONET-corrected SR. AERONET-corrected SR is
computed from the Level-1C Top-of-Atmosphere datausing a radiation transport model with input data
provided by AERONET. This analysis including aradiation transport model has to be completed by SR
measurements gathered during ad-hoc campaigns. One
aspect of potential synergy between Sentinel-2 andSentinel-3 validation of atmospheric correction cancover sharing of campaign data and organization of
joint ad-hoc campaigns. Finally, discussion about thevalidation protocol and statistical metrics currently
applied for reporting atmospheric correction
performance is of high interest.

************************
Sun-Induced Fluorescence and Spectral Vegetation
Indices for Heterogeneous Ecosystems and Diverse
Peatland Plant Communities************************

Bandopadhyay S1, Rastogi A1, Rascher U2, Rademske
P2, Schickling A2, Cogliati S3, Julitta T3, Celesti M3, Mac
Arthur A4, Burkart A2, Hueni A5, Damm A5, Tomelleri E6,Stróżecki M1, Sakowska K7, Gąbka M8, Rosadziński S8,
Sojka M9, Iordache M10, Reusen I10, Schuettemeyer D11,

Seasonality in solar induced chlorophyll fluorescenceand light use efficiency in boreal Finland

Nichol C1, Drolet G1, Porcar-Castell A2, Wade T1,

MacLellan C3, Levula J2, Mammarella I2, Vesala T2,
Middleton E4, Atherton J2
1
University Of Edinburgh, 2University of Helsinki, 3NERC
Spectroscopy Facility, 4NASA Goddard Space Flight
CentreSolar induced chlorophyll fluorescence has been shown
increasingly to be a useful proxy for the estimation ofgross primary productivity (GPP), with an emergence of
documented studies using ground based- airborne andsatellite retrievals. In the work presented here weaimed to explore the seasonality in a continuous timeseries of high resolution optical data, solar induced
fluorescence (hereafter SIF) retrievals and their relation
to gross primary production (GPP), canopy light use
efficiency (LUE) and pulse amplitude measures of
efficiency. SIF was calculated using infilling in two bands
from the incoming and reflected radiance using a pairof Ocean Optics USB2000+ spectrometers operated indural field of view mode, sampling at a 30 minute time
step using custom written automated software, fromearly spring through until autumn in 2011. The opticalsystem (see Drolet et al, 2014 for details) was mounted
adjacent to an eddy covariance system, over an 80m

Juszczak R

Poznan University of Life Sciences, Department ofMeteorology, 2Forschungszentrum Juelich GmbH,
Institute of Biogeosciences, IBG2, 3University of
Milano-Bicocca, Department of Earth andEnvironmental Sciences, 4University of Edinburgh,
School of Geosciences, 5University of Zurich,Department of Geography, 6Free University of
Bolzano/Bozen, Faculty of Science and Technology,
7
University of Innsbruck, Institute of Ecology, 8Adam
Mickiewicz University, Institute of Environmental
Biology, 9Poznań University of Life Sciences,
Department of Land Improvement, Env. Development
and Geodesy , 10Center for Remote Sensing and Earth
Observation Processes (VITO-TAP), 11European Space
Agency, ESTEC
Peatlands are one of the vital ecosystems of the earth
due to accumulation of carbon in the peat, big
biodiversity, and occurrence of distinctive vegetation
species. However, due to huge heterogeneity of thesurface, internal diversity, environmental gradients, it isalways a challenge to understand peatland vegetation
1

49

functionality through remotely sensed vegetation
indices (VIs) and sun-induced fluorescence (SIF) signals.
Previous studies of SIF were mostly restricting theirobservation on homogenous ecosystems like croplands,
grasslands, and forest areas. Hence, considering thisknowledge gap this study will demonstrate therelationships between VIs and SIF from heterogeneous
ecosystems and peatland vegetation communities
based on data collected during the SWAMP airborne
campaign in 2015.
Imaging spectrometer ‘HyPlant’ (the airborne
demonstrator for the ESA FLEX mission) was flown for
the first time over the extremely heterogeneous
peatland and surrounding ecosystems during the
SWAMP campaign held on 11th July 2015, within the
COST Action OPTIMISE, EUFAR, and ESA funded SWAMP
Summer school and under the FLEX-EU (ESA). Rzecin(POLWET) peatland is located in central-western Poland(Wielkopolska region) within Noteć Forest (52°45′ N
latitude,16°18′E longitude, 54 m asl). The entire Rzecin
peatland and its surroundings are enriched with diverse
vegetation groups of vascular and non-vascular plantcommunities. The target of this study is to explore acomparative analysis of SIF signals and VIs and theirrelationships obtained from different vegetation groups
at ecosystem level (forest, grassland, peatland) andfrom diverse peatland plants at plant communities
level. The VIs and Spectral Fitting Method (SFM)
retrieved SIF maps (O₂A and O₂B) were validated (VIs:
R² = 0.79-0.91; SIF: R² = 0.87-0.92) in support ofmeasured ground spectra before any analysis. A clear
positive trend with a good agreement (R² = 0.55-0.91)
and statistically significant (p<0.01) relations have been
observed between SIF bands (O₂A and O₂B) andgreenness indices (SR, NDVI) whereas, a negative trendwith a good agreement (R² = 0.40-0.71) and statisticallysignificant (p<0.01) relation have been found between
PRI and SIF at large scale vegetation group. Due to hugediversity and low SNR (Signal to Noise Ratio), no suchagreements were established between SIF bands andVIs at smaller scale peatland plant communities, except
for some isolated homogenous patches of meadows.
Filling the knowledge gap, this work provides a proof
that the relationships between SIF bands and several
VIs are very complex for heterogeneous ecosystems.

2016/21/B/ST10/02271 (Sun Induced florescence andphotosynthesis of peatland vegetation response tostress caused by water deficits and increased
temperature under conditions of climate manipulation
experiment).

************************Can We Measure Sun-Induced Chlorophyll
Fluorescence Emitted by Biocrusts?

Tagliabue G1, Panigada C1, Blanco Sacristán J1, Ladrónde Guevara M2, Celesti M1, Julitta T3, Maestre F4,
Miglietta F5, Rossini M1
1
University Of Milano - Bicocca, 2Centre for EcologicalResearch and Forestry Applications, 3JB Hyperspectral
Devices, 4Universidad Rey Juan Carlos, 5National
Research Council
Biocrusts, a combination of autotrophic andheterotrophic organisms including mosses, lichens,
liverworts, cyanobacteria and algae are a key
component of the semi-arid and arid regions of the
Earth. Besides playing a critical role in the stabilizationand development of drylands, biocrusts contribute
appreciably (~7%) to the global carbon fixation.
Nowadays, drylands cover about 45% of the Earth’s
land surface, and are expected to expand by up to 23%
by the end of this century. For these reasons,understanding biocrusts functioning and quantifying
their imprint on the global carbon dynamics is key toestablish ecosystem feedbacks to the climate system. In
this framework, Remote Sensing (RS) of sun-induced
chlorophyll fluorescence (F) might be a promising tool
for obtaining new insights into biocrusts functional
state.
In this contribution we aimed at understanding if the
weak F signal emitted by biocrusts can be passively
detectedusing
high-resolution
radiancemeasurements. In particular, this contribution aimed
at: i) quantifying the F emission of biocrusts at the red
and far-red emission peaks; ii) understanding therelative contribution of the different biocrust
components by relating the F signal to the fractional
cover of the endmembers.
At this purpose, we acquired high-spectral resolution
radiance measurements on 37 biocrust samples
collected in a dryland area located in central Spain(Aranjuez). The spectral measurements were collectedunder direct solar irradiance using the FLoX instrument(JB Hyperspectral Devices, Germany). The core of thissystem is a QEPro (Oceanoptics, USA) spectrometercovering the red and near-infrared regions (650-800nm), allowing to detect F at both the red and far-red
peak. The samples were measured before and after
watering in order to determine the effect of biocrusts
activation on the measured F signal. F was retrieved

Acknowledgment
The Research was co-funded by the COST Action ES1309
OPTIMISE, FP7 European Facility for Airborne Research(EUFAR),
FLEX-EU
ESA(Contract
No.
4000107143/12/NL/FF/If CCN3) and European Space
Agency which supported the SWAMP training course (616th of July 2015) and airborne campaign on 11th of
July 2015. Analyses of the data were supported by thePolish National Research Centre within the project No

50

using spectral fitting methods at the red and far-red
emission peaks.
Results showed that active biocrusts emit F with atypical two peaks spectrum. However, while vascularplants are typically characterized by a higher emission
in the far-red, biocrusts showed a higher signal in thered. This distinctive behavior is explained by thedifferent structure and chlorophyll content of biocrusts
compared to vascular plants and might be exploited todetect and monitor active biocrusts from remote.
Results also showed that moss-dominated biocrusts
emit higher F compared to lichen-dominated ones.
Overall, this analysis demonstrated the feasibility ofpassively detecting the faint F signal emitted by active
biocrusts, disclosing the possibility to obtain new
insights into biocrusts functional state. This opens great
opportunities to understand and monitor challenging
environments such as drylands from the local to theglobal scale.

model how E, L, and aRFL vary in the absence of theabsorption line. To do so, a precise function tointerpolate E, L, and aRFL inside the absorption line
needs to be defined. Accordingly, an accurateinterpolation strategy is needed, which takes into
account the following factors: (1) a good definition of
the starting point of each absorption band, (2) selectionof points outside the absorption bands to perform theinterpolation, and (3) an appropriate interpolation
method.
Given the variety of SIF retrieval methods at our
disposal, along with the methods´variables that can be
modified, it implies that multiple optimization options
have become available for obtaining precise SIF
retrieval. In order to streamline and automate thisprocess of fine tuning, it motivated us to develop a new
fluorescence retrieval toolbox called FLUOrescence
Retrieval Toolbox (FLUORT). FLUORT has beendeveloped in a GUI framework within the context ofAutomated Radiative Transfer Models Operator(ARTMO) scientific software package.
In FLUORT, we have implemented the most common SIF
retrieval methods available derived from the FLD,
extended FLD (eFLD), improved FLD (iFLD), Peak Height
Method (PHM) and Spectral Fitting Method (SFM). The
GUI interface allows the user to enter measurements ofradiance and irradiance data, and to choose between
any combination of retrieval and interpolation
methods. FLUORT first assesses the best bands forinterpolation, and after a first interpolation the user can
optimize: (1) the interval defined for limiting theabsorption bands, (2) the points used to take part in theinterpolation, (3) the interpolation method, and (4) the
free variables of the interpolation methods. The
toolbox directly shows the impact of the optimizationon the interpolated E, L, aRFL outputs.
In general, FLUORT automates the estimation of SIF at
the two oxygen absorption bands for each input
radiance and irradiance dataset. Moreover, in case theuser adds a reference SIF, a validation process can be
employed that compares the reference data against thecalculated one. After passing the beta phase, thetoolbox will become freely available to the community.

************************FLUORT: a GUI FLUOresence Retrieval Toolbox forautomating and optimizing sun-induced chlorophyll
fluorescence retrieval from spectroscopy data

Morcillo Pallarés P1, Cendrero-Mateo M1, Alonso L1,
Rivera Caicedo J2, Belda S1, Burriel H1, Moreno J1,
Verrelst J1
1
University Of Valencia - Laboratory for Earth
Observation (LEO), 2CONACYT-UAN, Secretariat of
Research and Postgraduate
Sun-induced chlorophyll fluorescence (SIF) is the lightre-emitted by plants in the red and far-red region of thespectrum following the light absorption byphotosynthetic pigments. The interest in SIF has
recently led to the creation of multiple spectroscopy
systems for the acquisition of this data at various scales,(ground-based, airborne or even spaceborne with theupcoming FLEX mission). However, a precise retrieval of
SIF is mandatory to enable using this subtle signal for
applications such as monitoring the plant’s
photosynthetic capacity. SIF retrievals methods are
based on incident solar irradiance and target radiancemeasurements. Hece, the main challenge relies in
disentangling the reflectance radiance (RFL) andemitted SIF from the measured target radiance (L).
To achieve this, most of the SIF retrieval methods
exploit the Fraunhofer line depth (FLD) principle. By
combining measurements of solar irradiance (E) and L(FLD and 3FLD) or E and apparent reflectance (aRFL =RFL + SIF) inside and outside the Fraunhofer line it ispossible to decouple SIF from RFL. A crucial step when
implementing the FLD approaches, however, is to************************

51

Sun-induced chlorophyll fluorescence: retrievals
methods and practical cases for proximal sensing.
Cendrero-Mateo M1, Wineke S2, Damm A3,4, Pinto F5,Alonso L1, Guanter L6, Celesti M7, Sabater N1,
Coglioatti S7, Julitta T8, Goulas Y9, Asen H10, PachecoLabrador J11, Mc rthur A12

retrievals methods (i.e. absorption bands range
selection, proper interpolation at the absorptions
bands, proper selection of the point inside de absorption
bands…) increase the uncertainty when retrieving F. The
aim of this work is to provide the scientific community areference study where they can evaluate the precisionof their F measurements based on both their instrument
configuration and the retrieval method used.

University Of Valencia, 2Centre of Excellence PLECO(Plant and Vegetation Ecology), Department of
Biology, University of Antwerp , 3Remote Sensing
Laboratories, Department of Geography, University of
Zurich, 4Department of Surface Waters – Research andManagement, Eawag, Swiss Federal Institute of
Aquatic Science and Technology, 5Global Wheat
Program, International Maize and Wheat Improvement
Center (CIMMYT), 6Helmholtz Center Potsdam, GFZ
German Research Center for Geosciences, Remote
Sensing Section, 7Remote Sensing of Environmental
Dynamics Laboratory, Università di Milano-Bicocca ,8
JB hyperspectral devices, 9French National Centre for
Scientific Research , 10Crop Science Group, Institute ofAgricultural Sciences, ETH Zurich, 11Max Planck
Institute for Biogeochemistry, 12University of
Edimburgh
The growing interest on the proximal sensing of sun‐
induced chlorophyll fluorescence (F) has been boosted inby space-based retrievals and up-coming missions such
as Earth Explorer of the European Space Agency
FLuorescence EXplorer (FLEX). In the last ten years, field
spectroradiometers have improved in spectral
resolution (Full Width Half Maximum, FWHM ≤ 0.3nm)
and signal-to-noise ratio (SNR ~ 1000:1). This currently
allows the exploitation of sophisticated retrieval
algorithms (e.g., spectral fitting methods) exploiting
resolved narrow absorption feature in the irradiancespectrum. However, F retrieval is very sensitive to
uncertainties, and results strongly depend on the
instrumentation, the measurement protocol and theretrieval method. In the last four years, the COST Action
ES1309 OPTIMISE “Innovative optical tools for proximal
sensing of ecophysiological processes” has gatheredefforts to address these three challenges in the proximal
sensing of F in three separated and connected works
submitted to this conference.
1************************
Instrumental considerations in the proximal sensingof sun‐induced chlorophyll fluorescence
Pacheco-Labrador J1, Hueni A2, Mihai L3, Alonso L4,
Julitta T5, Shakowska K6, Kuusk J7, Sporea D3, Burkart
A5, Goulas Y8, Cendrero-Mateo M4, Aasen H9, Mac
Arthur A10
1
Max Planck Institute for Biogeochemistry , 2Universityof Zurich, 3National Institute for Laser Plasma andRadiation Physics, 4University of Valencia, 5JB
hyperspectral devices, 6University of Innsbruck, 7Tartu
Observatory, 8French National Centre for Scientific
Research, 9ETH, 10University of Edinburgh
The growing interest on the proximal sensing of sun‐
induced chlorophyll fluorescence (F) has been boosted
in by space-based retrievals and up-coming missions
such as Earth Explorer of the European Space Agency
FLuorescence EXplorer (FLEX). In the last ten years, field
spectroradiometers have improved in spectral
resolution (Full Width Half Maximum, FWHM ≤ 0.3nm)
and signal-to-noise ratio (SNR ~ 1000:1). This currently
allows the exploitation of sophisticated retrieval
algorithms (e.g., spectral fitting methods) exploiting
resolved narrow absorption feature sin the irradiancespectrum. However, F retrieval is very sensitive to
uncertainties, and results strongly depend on the
instrumentation, the measurement protocol and theretrieval method. In the last four years, the COST Action
ES1309 OPTIMISE “Innovative optical tools for proximal
sensing of ecophysiological processes” has gatheredefforts to address these three challenges in theproximal sensing of F in three separated and connected
works submitted to this conference.

A major source of error when retrieving F is the proper
implementation of the different retrievals methods.
Thus before using F to understand vegetation dynamics
a precise retrieval of F is mandatory. This study is
divided in two sections; first, we evaluated theuncertainties in F retrievals (i.e. FLD approaches andSpectral Fitting Method, SFM) for a combination ofstate-of-the-art spectrometers suited to measure F (i.e.
ASD, MAYA, HR400, QEPRO). Secondly, we evaluated
how an erroneous implementation of the different

In these addresses the instrumental challenges in theproximal sensing of F. Spectroradiometers are passive
sensors sensitive to spectral radiation, as well as otherenvironmental variables. In this work we simulate astate-of-art spectroradiometer to model the impact ofdifferent instrumental noises and biases on the retrievalof F. We first combine a sensor emulator, experimental
and realistically simulated sensor responses to different
environmental variables and uncertainties to calibrate
synthetic sensor models. These are used to bias and52noise radiances featuring vegetation up-wellingradiance and solar down-welling radiances andevaluate their impact on the retrieval of F using spectral
fitting methods approach. First the impact of
uncertainty in the radiometric and spectral calibrations
is addressed, as well as the effect of different spectral
shifts. Then we evaluate the effects of thermallyinduced changes in spectral features and sensor
response (DRF), as well as non-linearity, and the
directional response function of the cosine diffuser.

which adds more complexity to the radiometricmeasurement procedure. Additionally, to properlyinterpret the signal also the light history (irradiance) is
important. Altogether, this requires properly calibrated
and characterized instruments, reliable measurement
setups, sophisticated measurement protocols, androbust retrieval methods that exceeds those of classicalspectral sampling. For the last four years, many
researchers have worked within the framework of an
European cooperation in science and technology (COST)
action ES1309 to meet the aforementioned challenge
by developing innovative optical tools for proximal
sensing of ecophysiological processes (OPTIMISE;
https://optimise.dcs.aber.ac.uk/). To make thisinformation available, the OPTIMISE community hascompiled three papers on instrument characterization(paper 1), measurement setups and protocols (paper 2),
and retrieval methods (paper 3). The aim of this work is
to provide the scientific community basic guidelines
towards a precise measurements of proximal sensing
sun‐induced chlorophyll fluorescence.

Results reveal the sensitivity of F retrieval to different
instrumental responses. Calibration uncertainties havelittle effect on the retrieval; however, spectral changes,
non-linearity and DRF present strong effects on F
retrieval that co-vary with the environmental drivers of
the sensor response. The effect of the different
phenomena on F retrieval is compared with the impact
on the reflectance factors, which results negligible inmost of the cases. This suggests that proximal sensingof F requires new and higher quality standards thanthose accepted in “traditional” proximal sensing
dedicated to the quantification of reflectance.
Quantification and development of such standards
should be prioritized considering the growing intereston F. Inadequate understanding and characterization of
instrumentation can lead to spurious results, where
instrumental responses to environmental variables areconfounded with physiological responses to the same
drivers. Uncertainties and biases on F proximal sensing
retrievals also jeopardize validation and scaling of F in
the context of the up-coming FLEX mission.

************************
Litchfield Savanna Supersite – A CEOS Land Process
Validation site in northern Australia

Maier SCharles Darwin University
22% of the global land surface are comprised of tropicalsavannas. Australia's savanna cover
approximately 1.9 million km2 which corresponds to
25% of Australia's land surface or 12% of theworld's savannas. Due to their highly dynamic naturesavannas are an important and sensitive
component of the global carbon and water cycle.
The Litchfield Savanna Supersite is located in northern
Australia's Top End approx. 80km south ofDarwin in Litchfield National Park. Situated in the mesic
tropical savanna the vegetation iscomprised of savanna woodland dominated by
Eucalyptus minata /tetrodonta with a grass and low
shrub understorey. Tree height ranges from 15-20m.
This makes the area representative for 90% ofAustralia's savanna. The site is flat with elevation
ranging from 203-228m above sea level over a
5km x 5km area.
Mean annual rainfall is 1420mm, of which 90% falls
between December and March. Thispronounced wet / dry season climate induces annual,
natural drought conditions. Together withfrequent disturbance through fire (every one to two
years) this creates a highly dynamic ecosystem.
Atmospheric conditions at the site range from veryclear and very dry in the early dry season to high1************************
Instrumental characterization, measurements
protocols, and retrievals methods in the proximal
sensing of sun‐induced chlorophyll fluorescence
Aasen H1, Cendrero-Mateo M2, Pacheco-Labrador J3,
Mac Arthur A4
1
ETH, 2University of Valencia, 3Max Planck Institute for
Biogeochemistry, 4University of Edinburgh
Space-based retrievals and up-coming missions such as
Earth Explorer of the European Space Agency
FLuorescence EXplorer (FLEX) have boosted thegrowing interest on the proximal sensing of sun‐
induced chlorophyll fluorescence (F) in. In the last ten
years, field spectroradiometers have improved inspectral resolution (Full Width Half Maximum, FWHM ≤0.3nm) and signal-to-noise ratio (SNR ~ 1000:1). Still, F
can only be measured at very narrow parts of thespectrum and the signal is small. Very precise
measurements (spectrally and radiometrically) ofradiance (L) and incident irradiance (E) are necessary

53

to FLEX to provide useful information for a proper
characterization of the atmosphere with theaccuracy required to retrieve the SIF signal. This
specific design of FLORIS gives the possibility tospectrally resolve the SIF spectrum in the 670 nm– 780 nm range for land applications. The FLEX
mission will observe mainly continental areas andterrestrial vegetation, but there is a growinginterest to understand the potential benefits in
exploiting FLEX observations to study andmonitor inland water bodies (i.e., lakes) andshallow costal waters. In fact, phytoplankton
contains chlorophyll pigments able to emit
fluorescence signal after solar light stimulation.
For this reason, it is interesting to understandwhether the FLEX technique developed for thevegetation, such as the Spectral Fitting (SF)method, can be further applied to aquatic
ecosystems after a proper adjustment.
In this framework, the aim of this work is toimplement and test the SIF retrieval algorithm
developed for vegetation applications (Cogliati etal., 2015) to model and fit the SIF signal in waterleaving radiance spectra. The SF approach was
initially revised in order to model theatmosphere-water radiation transfer (RT)interactions. To achieve this aim, we coupled theatmospheric RT model MODTRAN with the water
RT model Hydrolight. The latter code allows tosimulate several water bodies, characterized bydifferent optical and physical/chemical
properties. Inland waters are usually
parametrized following a four elements model:
pure water, bearing chlorophyll particles, Colored
Dissolved Organic Matters (CDOM) and Total
Suspended Matters (TSM). Radiance andreflectance upwelling spectra generated by the
coupled MODTRAN-Hydrolight model, in highspectral resolution (0,1 cm-1), were convolved to
the FLEX and S-3 spectral bands. Starting fromthis dataset, we applied the SF retrieval method,
adapted for aquatic ecosystem, to retrieve the
SIF. The results obtained on the simulated dataset
show the promising theoretical perspective to use
the FLEX technique also on water targets. This
preliminary results will be further compared anddiscussed in regard of real ground-based
experimental measurements recently acquired
during a number of field campaigns.

concentrations of absorbing aerosols (smoke) in a dry
atmosphere in the late dry season. The wet
season is typically characterised by very wet
atmospheric conditions. As rain events are occurring in
intense bursts the number of cloud free days is still
relatively high during the wet season.
Due to the site's local and global importance for the
carbon and water cycle the Terrestrial Ecosytem
Research Network (TERN) installed an eddy covariance
flux tower in 2015 to complement existing
long-term experiments monitoring canopy andunderstorey dynamics (leaf area index, leaf fall, leaf
litter decomposition). Furthermore, instruments formeasuring meteorological conditions and soil
moisture profiles have been installed. The installationof a soil moisture sensor grid is planned for2019.
Vegetation structure at the site has been characterised
through a number of airborne and groundbased Lidar data captures. Additionally, flora and faunasurveys are undertaken at regular intervals.
A program to regularly capture airborne hyperspectral
data coincident (within ±5min) with satellite
overpasses has been initiated in 2017. These data havebeen used for the validation of surface
reflectance from Sentinel-2/MSI, Terra/MODIS andAqua/MODIS. A suitable program for
capturing solar induced fluorescence is currently underdevelopment.

************************
Adapting the FLEX Fluorescence retrieval conceptfrom land vegetation to inland water

CESANA I1, BRESCIANI M2, COLOMBO R1, GIARDINO C2,

COGLIATI S1Remote Sensing of Environmental Dynamics Lab.,DISAT, University Of Milano-Bicocca, 2CNR-IREA,
Institute for Electromagnetic Sensing of theEnvironment
1

The FLEX (FLuorescence EXplorer) satellite
mission, under preparation by the European
Space Agency (ESA) within the Earth Explorer
program, aims to observe the sun-induced
chlorophyll fluorescence signal (SIF) emitted byterrestrial plants. The FLuORescence Imaging
Spectrometer (FLORIS) aboard of the FLEX
satellite is specifically designed to provide
radiance observations in high-spectral resolution(0,3 nm) around the O2 bands (687 nm and 760,4nm), together with a broad spectral coverage
from 500 nm to 780 nm (visible-NIR wavelength
range). The Sentinel-3 satellite will fly in tandem
54