# Ground Based Hyperspectral Imaging to Characterize Canopy-Level Photosynthetic Activities
## 1 Introduction
These parameters can be used to calculate the maximum (\(\frac{F_{v}}{F_{m}}\) or \(\frac{F_{p}^{\prime}}{F_{m}}\)) and operating (\(\frac{F_{q}^{\prime}}{F_{m}}\), also known as, \(\Phi_{PSII}\)) efficiencies of PSII photochemistry, both of which are useful for photosynthetic efficiency evaluation and plant stress detection [14]. There are active and passive sensing approaches to measure chlorophyll fluorescence parameters. Active techniques include pulse amplitude modulation (PAM) [15] and laser induced fluorescence transience (LIFT) [16], both of which can emit predefined light to measure minimal fluorescence (\(F_{0}\)), steady state fluorescence (\(F_{s}\)), and maximal fluorescence (\(F_{m}\)), and can calculate variable fluorescence (\(F_{p}\)). Based on active techniques, portable instruments (e.g., PAM fluorometers) have been developedand widely used for photosynthesis studies [17; 18; 19; 20; 21; 22]. Active techniques rely on artificial illumination, however, which limits their use for large scale applications [23]. Passive techniques retrieve chlorophyll fluorescence emission excited by solar illumination (natural sunlight), which is termed solar induced fluorescence or sun induced fluorescence (SIF). Upwelling radiance from plants under solar illumination is a mixture of SIF and surface reflectance, and it is feasible to decouple SIF signals from the upwelling radiance in Fraunhofer lines of the solar spectrum in which irradiance is substantially reduced because of atmospheric absorption (e.g., hydrogen and oxygen). In the red and far-red spectral range, three Fraunhofer lines are frequently used for SIF retrieval, including \(H\alpha\) at 656 nm because of hydrogen and \(O_{2}\)-\(B\) at 687 nm and \(O_{2}\)-\(A\) at 760 nm because of oxygen. Common SIF retrieval approaches include conventional Fraunhofer line discrimination (FLD), improved FLD variants, and reflectance-based ratios [24]. Many studies explored the use of ground based spectrometers to retrieve the SIF values of plant leaves, and reported high correlations between SIF measurements and fluorescence measured using active techniques (e.g., PAM fluorometers) [25; 26; 27; 24]. Large national research institutions (e.g., the European Space Agency, the EPA, and the National Aeronautics and Space Administration (NASA)) launched programs to investigate the use of hyperspectral imagery sensed remotely from planes and satellites to monitor SIF changes at the regional and global levels, to estimate carbon fixation (or flux of carbon dioxide) and gross primary productivity (GPP). Multiple studies have shown strong correlations between gross primary productivity (whole canopy photosynthesis) and SIF through various modeling methods [28; 29; 12]. When using SIF to track GPP, there is usually a strong association with the absorbed photosynthetically active radiation (PAR). In situations where light intensity is constant and extreme stress (such as heat stress) limits canopy photosynthesis, however, the relationship is somewhat degraded, because excess energy that cannot be dissipated through non-photochemical quenching (NPQ) might be emitted as increased fluorescence [30]. Thus, it is important to develop a method to generate canopy level quantum yields and photosynthetic activities if the method can be broadly applicable under a range of environmental conditions. These data would be invaluable for research studies and policy-making to secure the food supply [28; 29; 31; 32; 33]. Spectrometer-based approaches can provide the highest accuracy of measurement location (a specific point on a leaf), but have an obvious limitation in the scanning throughput (point by point). By contrast, airborne and spaceborne solutions provide a substantially faster scanning throughput, but have compromised spatial resolutions (sub-meter to meters). Neither approach, therefore, would be suitable for breeding programs and plant-science studies at the canopy or sub-canopy levels.