Development of a Vegetation Fluorescence Canopy Model
Project funded by the European Space Agency
ESA-ESTEC contract no. 16365/02/NL/FF
Overview

A study was launched in October 2002 by the European Space Agency (ESA) to advance the underlying science of a possible future vegetation fluorescence space mission by addressing the need for an integrated canopy fluorescence model. The objective of this study was to review and advance existing fluorescence models at the leaf level and to integrate these into canopy models in order to simulate the combined spectral reflected radiance and fluorescence emission signals. This model has been developed with the aid of new and existing laboratory and field campaign measurements.

This Website provides the software and related publications developed under the FluorMOD project, describing the background for the choice of the leaf-level and canopy-level models which have been adapted for simulation of the fluorescence emission that is added to the canopy radiance signal. The model is based on a modified version of PROSPECT (FluorMODleaf) which includes an elementary fluorescence emission spectrum and allows a dependence on some physiological variables, e.g., canopy temperature and illumination light levels. The canopy model is based on the turbid medium SAIL model (FluorSAIL), modified to internally compute the illumination levels through the canopy, to couple with FluorMODleaf, and through MODTRAN, to provide a means of simulating incoming irradiance at the top of the canopy as well as the upwelling radiance above the atmosphere at spectral resolution of 1 nm in the 400 to 1000 nm wavelength range. Further, a graphical user interface has been developed (FluorMODgui) as a consistent means of linking leaf and canopy simulations for evaluation and validation of the fluorescence model between team members and the community with the idea of continuing understanding the leaf model, canopy model, and the nature of the physiological controls.



Team Members and Collaborators

J.R. Miller, York University, Canada - Principal Investigator – jrmiller@yorku.ca
 M. Berger, ESA-ESTEC, The Netherlands - Project Manager – Michael.Berger@esa.int

 Leaf Model Development – FluorMODleaf
S. Jacquemoud, U. Paris, France – jacquemo@ccr.jussieu.fr
R. Pedrós, U. Paris/LURE, France – Roberto.Pedros@uv.es
I. Moya, LURE, France – moya@lure.u-psud.fr
Y. Goulas, LURE, France –  Yves.Goulas@lure.u-psud.fr
J. Louis, LURE, France – Juliette.louis@lure.u-psud.fr

 Canopy Model Development – FluorSAIL
W. Verhoef, NLR, The Netherlands – verhoef@nlr.nl

 Leaf-Canopy Model Interface Development – FluorMODgui
P.J. Zarco-Tejada, IAS-CSIC, Spain – pzarco@ias.csic.es

 Physiological and Environmental Drivers of Chlorophyll Fluorescence
G. Mohammed, P&M Technologies, Canada – mohammed@onlink.net
I. Moya, LURE, France – moya@lure.u-psud.fr

Model Validation Experiments and Lab/Field Data Collection
J. Moreno, U. Valencia, Spain – Jose.Moreno@uv.es
I. Moya, LURE, France – moya@lure.u-psud.fr
P.J. Zarco-Tejada, IAS-CSIC, Spain – pzarco@ias.csic.es


Project Reports

Miller, J.R., Berger, M., Goulas, Y., Jacquemoud, S., Louis, J., Moise, N., Mohammed, G., Moreno, J., Moya, I., Pedrós, R., Verhoef, W., and Zarco-Tejada, P.J., Development of a Vegetation Fluorescence Canopy Model, ESTEC Contract No. 16365/02/NL/FF, Final Report, May 2005. Download the final report in PDF here.


Background Fluorescence Literature

During the course of the project the fluorescence literature was reviewed and consulted extensively, as included in the reference in the FluorMOD report. Links to this literature is provided for the convenience of the interested community. Download the reference list in PDF here.


Relevant Publications

In this section you can find published material presented at Conferences, Simposia and Journals related to this research project.

Miller, J.R., Berger, M., Alonso, L., Cerovic, Z., Goulas, Y., Jacquemoud, S., Louis, J., Mohammed, G., Moya, I., Pedrós, R., Moreno, J., Verhoef, W., Zarco-Tejada, P.J., Progress on the Development of an Integrated Canopy Fluorescence Model, 2003 International Geoscience and Remote Sensing Symposium, IGARSS'03, pp. 601-603 Vol.1, ISBN 0-7803-7929-2 - 0-7803-7930-6, Toulouse (France), 21-25 / 7 /2004.

Miller, J.R., Berger, M., Jacquemoud, S., Moreno, J., Mohammed, G., Moya, I., Pedrós, R., Verhoef, W., Zarco-Tejada, P.J., Alonso, L., Goulas, Y., and Louis, J. (2004), Overview of FluorMOD: A Project to Develop an Integrated Leaf-Canopy Fluorescence Simulation Model, 2nd International Workshop on Remote Sensing of Vegetation Fluorescence, 17-19 Nov. 2004, Montreal (Canada).

Pedrós, R., S. Jacquemoud, Y. Goulas, J. Louis, I. Moya, A New Leaf Fluorescence Model, 2nd International Workshop on Remote Sensing of Vegetation Fluorescence, 17-19 Nov. 2004, Montreal, Canada.

Verhoef, W., Extension of SAIL to Model Solar-Induced Canopy Fluorescence Spectra, 2nd International Workshop on Remote Sensing of Vegetation Fluorescence, 17-19 Nov. 2004, Montreal, Canada.

Zarco-Tejada P.J., Pérez-Priego O., Sepulcre-Cantó G., Miller J.R., and Fereres E. (2005), Chlorophyll Fluorescence Detection with a High-Spectral Resolution Spectrometer through in-filling of the O2-A band as function of Water Stress in Olive Trees, 2nd International Workshop on Remote Sensing of Vegetation Fluorescence, 17-19 Nov. 2004, Montreal (Canada).
Zarco-Tejada, P.J., J.R. Miller, R. Pedrós, W. Verhoef, and M. Berger, FluorMODgui: A Graphic User Interface for the Spectral Simulation of Leaf and Canopy Fluorescence Effects, 2nd International Workshop on Remote Sensing of Vegetation Fluorescence, 17-19 Nov. 2004, Montreal, Canada.

Zarco-Tejada, P.J., J.R. Miller, R. Pedrós, W. Verhoef, and M. Berger, FluorMODgui V3.0: A Graphic User Interface for the Spectral Simulation of Leaf and Canopy Chlorophyll Fluorescence, Computers & Geosciences (submitted).



Software Download
The FluorMODleaf leaf model, FluorSAIL canopy model, and FluorMODgui Graphic User Interface software can be downloaded here.
The FluorMODgui is a Graphic User Interface (GUI) software package developed within the frame of the FluorMOD project which enables simulation of leaf and canopy reflectance with the effects of chlorophyll fluorescence, running the leaf and canopy models (dubbed FluorMODleaf and FluorSAIL) independently and through a coupling scheme. Inputs for the FluoMODleaf layer are N (number of leaf layers, as in PROSPECT), Cab (chlorophyll a+b content), Cw (water equivalent thickness), Cm (dry matter content), Fi (fluorescence quantum efficiency), T (temperature), S (species type), and Sto (stoichiometry of the Photosystem II to Photosystem I reaction centers). Inputs for the FluorSAIL canopy are (i) those generated by FluorMODleaf: leaf reflectance & transmittance spectra, excitation-fluorescence response matrix (back & forward),  (ii) a specification of light response: 2 PAR-dependent coefficients, and (iii) parameters used to specify illumination conditions, canopy structure, and constraints: a MODTRAN4 6-parameter spectra, solar zenith angle, viewing zenith & relative azimuth angles, a soil reflectance spectra, canopy, LAI and LIDF parameters, and a hot-spot parameter. Outputs for the linked leaf-canopy fluorescence model are the leaf spectral reflectance, transmittance, and canopy reflectance with and without the fluorescence signal. Current software developments enable multiple runs to simulate diurnal effects under different viewing geometries.
The user is encouraged to read the final project report and publications listed in this website for reference to model design and current limitations. Feedback and results from validation studies are encouraged in order to improve the models developed as part of FluorMOD.


The FluorMODgui Graphic User Interface software can be downloaded here.
Please read the License Agreement for FluorMOD models downloaded here

      


License Agreement for FluorMODgui v3.1 (FLUORMOD Graphic User Interface), LeafMOD v3.0 (Leaf Fluorescence Model), and FluorSAIL v2.2 (Canopy Fluorescence Model).

Permission is hereby granted, without written agreement and without license or royalty fees, to use, copy, modify, and distribute this software and its documentation for research purposes, provided that the authors of this work are properly cited, and that the following two paragraphs appear in all copies of this software.

PROJECT FUNDED BY THE EUROPEAN SPACE AGENCY (ESA) UNDER ESTEC CONTRACT No. 16365/02/NL/FF, "Development of a Vegetation Fluorescence Canopy Model". IN NO EVENT SHALL THE EUROPEAN SPACE AGENCY (ESA) NOR ANY OF THE INSTITUTIONS ("The Institutions") INVOLVED IN THE DEVELOPMENT OF FluorMOD MODELS BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OF, OR INABILITY TO USE, THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF SUCH INSTITUTIONS HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ESA AND THE INSTITUTIONS INVOLVED IN THIS PROJECT SPECIFICALLY DISCLAIM ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE INSTITUTIONS HAVE NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.



Please send comments and feedback to pzarco@ias.csic.es
Last update 4 May 2005