# FluoC Spec 2--An Automated Field Spectroscopy System to Monitor Canopy Solar-Induced Fluorescence
## 2 Materials and Methods  
### Instrument Design  
The core element of FluoCSpec 2 (Figure 1) is an ultra-high resolution spectrometer (QEpro, OceanOptics Inc., Dunedin, FL, USA) that is customized to measure radiation in the fluorescence emission wavelength range (650-800 nm). This represents the key difference between FluoCSpec 2 and FluoCSpec, which uses HR2000+, a spectrometer without temperature control and thus has a lower signal-to-noise ratio (~250:1). Given a specific grating (and thus the groove density), there is a trade-off between the spectral range and spectral resolution (Full-Width at Half Maximum, FWHM). Thus, in practice, to achieve a resolution that allows for SIF retrievals using narrow Fraunhofer lines, a spectral resolution close to ~0.1-0.3 nm is necessary [44]. A common misconception is to equate the spectral sampling interval with the spectral resolution. The spectral sampling interval is the difference in wavelength between two consecutive data points, which is usually half to one-third of the spectral resolution. Given a known spectral range (\(\Delta\lambda\)) and the number of pixels (N) of a spectrometer, we can calculate the dispersion (D') of the spectrometer as:  
\[\mathrm{D^{\prime}}=\Delta\lambda/\mathrm{N}, \tag{1}\]  
Since QEpro is not an imaging spectrometer, each pixel on the detector collect the photons from a specific wavelength. This is different from the nomenclature commonly used in the remote sensing community, in which pixels refer to a unit area on an image. We can calculate the spectral resolution (FWHM) as the product of dispersion and pixel resolution (P), which is a function of the slit size. Pixel resolutions of spectrometers are usually provided by the manufacturers. The slit size affects both FWHM (Equation (2)) and the signal received by the detector per second. A larger slit size means coarser FWHM but increases the number of photons that reach the detector per unit time and thus can reduce the integration time:  
\[\mathrm{FWHM}=\mathrm{D^{\prime}}\times\mathrm{P}, \tag{2}\]  
In the meantime, key spectral windows where SIF is often retrieved need to be covered. In our case, we chose the near-infrared region (730-780 nm) where both the narrow Fraunhofer lines near 750 nm and the wide oxygen absorption band (O\({}_{2}\)-A, centered around 760 nm) are covered. The setting enables the retrieval of the NIR SIF at an FWHM of ~0.14 nm. If red SIF retrieval is needed, the spectrometer can be customized to cover the red region (650-730 nm). If the retrieval of both oxygen bands is intended, then the spectrometer can be customized to cover both O\({}_{2}\)A and O\({}_{2}\)B (centered around 687 nm) bandswith a coarser resolution (\(\sim\)0.4 nm). An additional spectrometer (HR2000 or FLAME, OceanOptics Inc., Dunedin, FL, USA) can be added to the system to measure the canopy reflectance between 400 and 1100 nm at a spectral resolution of around 3 nm. The QEpro has an internal shutter which closes when dark current measurements are needed. As we will show later, routine dark signal measurements are not necessarily needed if the detector's temperature and the integrating time are known. QEpro has 1044 pixels, including 1024 active pixels, eight dummy pixels, and twelve optical dark pixels on the edge of the detector. The first four and last four pixels are intentionally blocked and thus, not optically active (i.e., do not respond to incoming radiation). Then, there are six pixels each after the first four and before the last four that are optically active but not used. We use only the 1024 pixels in the middle. Measurements of both incoming solar radiation and canopy radiation are needed to retrieve SIF. FluoSpec 2 uses an optical shutter (FOS 2 \(\times\) 2 TTL, OceanOptics Inc., Dunedin, FL, USA) and a fiber splitter to achieve this task. The spectrometer sends a programmed electronic signal (high or low) to the optical shutter, which opens one port at a time. Each port on the shutter is connected to one leg of the fiber splitter.