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Systematic Assessment of Retrieval Methods for Canopy Far-Red Solar-Induced Chlorophyll Fluorescence Using High-Frequency Automated Field Spectroscopy

Chang, Christine Y. and Guanter, Luis and Frankenberg, Christian and Köhler, Philipp and Gu, Lianhong and Magney, Troy S. and Grossmann, Katja and Sun, Ying (2020) Systematic Assessment of Retrieval Methods for Canopy Far-Red Solar-Induced Chlorophyll Fluorescence Using High-Frequency Automated Field Spectroscopy. Journal of Geophysical Research: Biogeosciences, 125 (7). Art. No. e2019JG005533. ISSN 2169-8953.

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Remote sensing of solar‐induced chlorophyll fluorescence (SIF) offers potential to infer photosynthesis across scales and biomes. Many retrieval methods have been developed to estimate top‐of‐canopy SIF using ground‐based spectroscopy. However, inconsistencies among methods may confound interpretation of SIF dynamics, eco‐physiological/environmental drivers, and its relationship with photosynthesis. Using high temporal‐ and spectral resolution ground‐based spectroscopy, we aimed to (1) evaluate performance of SIF retrieval methods under diverse sky conditions using continuous field measurements; (2) assess method sensitivity to fluctuating light, reflectance, and fluorescence emission spectra; and (3) inform users for optimal ground‐based SIF retrieval. Analysis included field measurements from bi‐hemispherical and hemispherical‐conical systems and synthetic upwelling radiance constructed from measured downwelling radiance, simulated reflectance, and simulated fluorescence for benchmarking. Fraunhofer‐based differential optical absorption spectroscopy (DOAS) and singular vector decomposition (SVD) retrievals exhibit convergent SIF‐PAR relationships and diurnal consistency across different sky conditions, while O₂A‐based spectral fitting method (SFM), SVD, and modified Fraunhofer line discrimination (3FLD) exhibit divergent SIF‐PAR relationships across sky conditions. Such behavior holds across system configurations, though hemispherical‐conical systems diverge less across sky conditions. O₂A retrieval accuracy, influenced by atmospheric distortion, improves with a narrower fitting window and when training SVD with temporally local spectra. This may impact SIF‐photosynthesis relationships interpreted by previous studies using O₂A‐based retrievals with standard (759–767.76 nm) fitting windows. Fraunhofer‐based retrievals resist atmospheric impacts but are noisier and more sensitive to assumed SIF spectral shape than O₂A‐based retrievals. We recommend SVD or SFM using reduced fitting window (759.5–761.5 nm) for robust far‐red SIF retrievals across sky conditions.

Item Type:Article
Related URLs:
URLURL TypeDescription
Chang, Christine Y.0000-0001-6609-3527
Guanter, Luis0000-0002-8389-5764
Frankenberg, Christian0000-0002-0546-5857
Köhler, Philipp0000-0002-7820-1318
Gu, Lianhong0000-0001-5756-8738
Magney, Troy S.0000-0002-9033-0024
Grossmann, Katja0000-0002-5154-197X
Sun, Ying0000-0002-9819-1241
Additional Information:© 2020 American Geophysical Union. Received 23 OCT 2019; Accepted 22 APR 2020; Accepted article online 25 APR 2020. We are grateful to our anonymous reviewers for constructive suggestions, to Joseph Skovira for significant contributions to design and deployment of the bi‐hemispherical system, to Ari Kornfeld for contributions to SIF retrieval code, and to Jochen Stutz for significant contributions to deployment and data analysis for the PhotoSpec. This work is funded by the USDA‐NIFA postdoctoral fellowship to C. Y. C. (2018‐67012‐27985). This material is based upon work that is supported by the National Institute of Food and Agriculture, U.S. Department of Agriculture, Hatch under 1014740. Y. S., C. F., and P. K. acknowledge the NASA Earth Science Division MEaSUREs program. C. F. and P. K. are funded by the Earth Science U.S. Participating Investigator (Grant: NNX15AH95G). This research is also supported by the US Department of Energy (DOE), Office of Science, Biological and Environmental Research Program. ORNL is managed by UT‐Battelle, LLC, for DOE under contract DE‐AC05‐00OR22725. Following AGU policy, the PhotoSpec data used in this study are publicly available at a data repository hosted at the California Institute of Technology ( and associated with DOI Data from the bi‐hemispherical system are publicly available at a data repository hosted by Cornell University ( and associated with DOI Code used for SIF retrievals can be found on Github ( and is associated with DOI
Funding AgencyGrant Number
Department of Agriculture (USDA)2018-67012-27985
Department of Agriculture (USDA)1014740
Department of Energy (DOE)DE-AC05-00OR22725
Subject Keywords:solar‐induced chlorophyll fluorescence (SIF); assessment of retrieval methods; field spectroscopy
Issue or Number:7
Record Number:CaltechAUTHORS:20200427-104210993
Persistent URL:
Official Citation:Chang, C. Y., Guanter, L., Frankenberg, C., Köhler, P., Gu, L., Magney, T. S., et al. (2020). Systematic assessment of retrieval methods for canopy far‐red solar‐induced chlorophyll fluorescence using high‐frequency automated field spectroscopy. Journal of Geophysical Research: Biogeosciences, 125, e2019JG005533.
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:102799
Deposited By: Tony Diaz
Deposited On:27 Apr 2020 17:59
Last Modified:02 Mar 2021 21:20

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