# FluoC Spec 2--An Automated Field Spectroscopy System to Monitor Canopy Solar-Induced Fluorescence
## 2 Materials and Methods
### Calibrations and SIF Retrieval  
Before the system was used in the lab or field tests, a few calibration and modifications were needed to ensure the highest data quality was obtained. First, a wavelength calibration was needed to make sure that the spectra from both channels (solar and vegetation) were aligned. It is possible to do this with a light source with known emission peaks, for example, a mercury-argon light. Argon has at least four strong emission peaks in the 730 to 780 nm range to ensure proper wavelength calibration. Essentially, wavelength calibration establishes a polynomial relationship between the pixel number of the CCD detector in the spectrometer and the actual wavelength:  
\[\lambda_{\mathrm{P}}=\lambda_{0}+\mathrm{C_{1}P}+\mathrm{C_{2}P^{2}}+\mathrm{ C_{3}P^{3}}, \tag{3}\]  
\(\lambda_{\mathrm{P}}\) is the wavelength of pixel number p. \(\lambda_{0}\) is the wavelength of the first pixel. \(\mathrm{C_{1}}\), \(\mathrm{C_{2}}\), and \(\mathrm{C_{3}}\) are coefficients that can be derived from the calibration. During the calibration, \(\lambda_{\mathrm{P}}\) and p are recorded, and the rest of the parameters are derived from the least square optimization. An excel spreadsheet for calculating the wavelength calibration parameters is available on Github (the link is available in the acknowledgement). Radiometric calibration of FluoSpec 2 needs to be done on both the fiber connected to the upward cosine corrector and the downward bare fiber that points to the vegetation canopy. Calibration of the bare fiber is done with a homogenous light source with known intensity. We recommend using an integrating sphere, and in our case, the Labsphere HELIOS 8 inch integrating sphere (Labsphere,  
Figure 2: Lab tests of FluoSpec 2. (**A**) Calibration Factors estimated using FluoSpec 2 and the HELIOS integrating sphere. The calibration factors were collected under various integration times. (**B**) The ratio between calibration factors at 500 ms, 400 ms, and 300 ms. (**C**) Lab set-up when calibrating FluoSpec 2 and testing whether the shutter is “light-tight”. (**D**) Digital numbers (DNs) measured at various light intensities. The attenuator is fully open at 0%, and the light intensity in this setting is twice the intensity of peak solar radiation. North Sutton, NH, USA) was used. The raw data and dark current at various integration time were recorded, and the calibration factor was calculated as  
\[Cal_{BF}=\frac{RAD}{Raw-Dark}, \tag{4}\]  
_RAD_ is the radiance of the light source, which is provided by the integrating sphere. _Raw_ is the digital number measured by FluoSpec 2 when the light source is on and the shutter of QEpro is off. _Dark_ is the dark current measured when the internal shutter of QEpro is closed. _CalBF_ is the calibration factor, which is a function of wavelength and integration time. We made measurements under various integration times to examine whether the calibration factor obtained at one integration time can be used to calculate the calibration factor at other integration times. This is important because field measurements are made at various integration times (see Data Acquisition). Similarly, we calculated the calibration factor for the cosine corrector using a tungsten-halogen light source (HL-3P-CAL, OceanOptics, Inc.). Once the calibration is done, it is important to keep the light path intact, i.e., fiber optics should not be detached from the spectrometer and the shutter. Alternatively, FluoSpec 2 can be assembled in the field, and calibrated using the cross-calibration approach below. In-field radiometric calibration of FluoSpec 2 can be challenging. An integrating sphere as large as HELIOS is difficult to deploy in the field. It is even more challenging once instruments are installed on tall towers with limited space on the top. Here we provide a relatively simple approach-a cross-calibration methodin which a separate spectrometer that has been calibrated with the integrating sphere in the lab is used as a reference to calibrate FluoSpec 2.