This article has been accepted for inclusion in a future issue of this journal. Content is final as presented, with the exception of pagination. IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING 1 Solar-Induced Chlorophyll Fluorescence Measured From an Unmanned Aircraft System: Sensor Etaloning and Platform Motion Correction Juliane Bendig , Zbynˇ ek Malenovský , Deepak Gautam, and Arko Lucieer Abstract— A dual-field-of-view spectroradiometer system has been developed for measuring solar-induced chlorophyll fluo- rescence (SIF), from an unmanned aircraft system (UAS). This “AirSIF” system measures spectral reflectance in the visible and near-infrared wavelengths as well as SIF in far-red O2-A and red O2-B absorption features at high spatial resolution. It has the potential to support the interpretation and validation of canopy-emitted SIF observed by airborne, and future spaceborne sensors at coarser spatial resolutions, as well as simulated by radiative transfer models. In this contribution, we describe the AirSIF data collection and processing workflows and present a SIF map product of spatially explicit and geometrically correct spectroradiometer footprints. We analyze two possible sources of error in SIF retrieval procedure: a sensor-specific spectral artifact called etaloning and the uncertainty of incoming irradiance during UAS flight due to airframe motion (pitching and rolling). Finally, we present results from two SIF acquisition approaches: a continuous mapping flight and a stop&go flight targeting predefined areas of interest. The results are analyzed for a case study of Alfalfa and grass canopies and validated against ground measurements using the same system. Index Terms— Airborne spectroscopy, solar-induced chloro- phyll fluorescence (SIF), unmanned aerial vehicle (UAV). I. I NTRODUCTION S OLAR-INDUCED chlorophyll fluorescence (SIF) has become a recent focus point of optical remote-sensing research. The quantitative mapping of SIF satellite data acquired with GOME-2 [1], GOSAT [2], OCO-2 [3] , and more recently the TROPOspheric Monitoring Instrument (TROPOMI) [4] revealed the potential to enhance our under- standing of terrestrial vegetation gross primary production and Manuscript received May 17, 2019; revised August 11, 2019 and Octo- ber 21, 2019; accepted November 22, 2019. This work was supported by the Australian Research Council within the Discovery Grant under Grant DP140101488: Air LIFT (support for Arko Lucieer, Deepak Gautam and infrastructure). The work of J. Bendig was supported by the German Research Foundation (DFG) Scholarship under Project 289370018. The work of Z. Malenovský was supported by the Australian Research Council Future Fellowship “Bridging Scales in Remote Sensing of Vegetation Stress” under Grant FT160100477. (Corresponding author: Juliane Bendig.) J. Bendig, Z. Malenovský, and A. Lucieer are with the College of Sciences Engineering and Technology, School of Technology, Environ- ments and Design, University of Tasmania, Hobart, TAS 7005, Aus- tralia (e-mail: juliane.bendig@utas.edu.au; zbynek.malenovsky@utas.edu.au; arko.lucieer@utas.edu.au). D. Gautam is with the School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA 5064, Australia (e-mail: deeepak.gautam@adelaide.edu.au). Color versions of one or more of the figures in this article are available online at http://ieeexplore.ieee.org. Digital Object Identifier 10.1109/TGRS.2019.2956194 consequently the global carbon cycle [5]. Early studies on SIF retrieval triggered the development of novel SIF detecting airborne platforms [6], [7] and new satellite missions like the European Space Agency’s Earth Explorer FLEX [8]. These new initiatives have raised questions regarding the interpretation and validation of a fluorescence signal collected by the satellite. One of the main challenges is the scaling of fluorescence measurements from the leaf to the canopy level. Although the leaf level is relatively well-understood [9], the interpretation of canopy SIF observations is more complicated due to the canopy architecture. Multiple scattering by vegetation structures (e.g., leaves and stems) is increasing the reabsorption of the red SIF signal [10]. Additionally, sun-lit leaves produce higher SIF intensity due to experiencing higher levels of radiance than the shaded leaves under weaker, diffuse illumination [11]. Recent modeling work has demonstrated that leaf-to-canopy SIF scaling can be studied and resolved using radiative transfer models [12]–[15], however, in situ data are required to calibrate and validate both models and satellite data. Ground- and tower-based systems can provide spatially detailed, site-specific SIF data [16], [17], but they only measure a limited area within their footprint. SIF observations from unmanned aircraft systems (UASs) may provide high-resolution and spatially explicit data from relatively short observational distances (e.g., 10–30 m) [18] and thus complement the high altitude chlorophyll fluores- cence remote sensing. Although Burkart et al. [19] developed a UAS-based SIF system already in 2014, UAS that can deliver both accurate spectral data as well as accurate spatial charac- terization of the spectroradiometer’s footprint location, shape, and size is lacking. Burkart et al. [19], Garzonio et al. [20], Zarco-Tejada et al. [21] used instruments, which were spec- trally less stable (uncooled sensor chip) and with coarser spec- tral resolution (full width at half maximum (FWHM) of 1.5, 1.5, and 6 nm), both key factors for reliable SIF retrieval [22]. Other studies used spectrally optimal spectroradiometers, but the UAS solution was lacking the positioning and orientation of sensors and associated geometric processing workflow for an accurate ground projection of the spectroradiometer’s field of view (FOV) [23]. Here, we present a system that enables both: SIF retrieval from a spectroradiometer with a suitable spectral resolution (FWHM of 0.8 nm) and accurate geoloca- tion of the SIF measurements enabling further spatial analysis. Retrieval of a weak SIF signal is challenging, especially with regard to radiometric stability of the measurements. 0196-2892 © 2019 IEEE. Personal use is permitted, but republication/redistribution requires IEEE permission. See http://www.ieee.org/publications_standards/publications/rights/index.html for more information.