# FluoC Spec 2--An Automated Field Spectroscopy System to Monitor Canopy Solar-Induced Fluorescence
## 2 Materials and Methods
### Instrument Design
On the other side of the shutter, ports are connected to fiber optics, one of which measures incoming radiation with a cosine corrector (CC-3, OceanOptics Inc., Dunedin, FL, USA) while the other one measures upwelling radiation from the vegetation canopy from a nadir view. The field-of-view of the downward-looking fiber is 25 degrees. The radius of the area that is measured by the system can then be calculated as h \(\cdot\) tan(25/2), where h is the distance between the sensor and the vegetation canopy. When installing a sensor in an ecosystem with sparse canopies, we use a cosine corrector on the downward-looking fiber. In this way, a larger area can be observed, although it should be noted that leaves in the observed area do not contribute equally to the signal received by the sensor (weighted by the cosine of incident angle) [45]. An air conditioner is used to keep the enclosure at a stable temperature. Depending on the local weather and the desired cool down rate (degrees below ambient), the power need of the air conditioner varies. The power consumption of FluoSpec 2 without the air conditioner is \(\sim\)15 W at its maximum (data not shown). Depending on the site location, the power need for the air conditioner varies and thus, the power consumption can vary from 50 W to 200 W. Adding a shading mechanism, installing the enclosure in the understory of a forest, or using a highly reflective surface will help to reduce the radiation load on the enclosure. QEpro has a TEC (Thermal Electric Cooler) that can further cool down  
Figure 1: The design of FluoSpec 2. (**A**) An example of the system with both a solar-induced chlorophyll fluorescence (SIF) spectrometer and a reflectance spectrometer; (**B**) FluoSpec 2 on a 40-m tower in central Virginia; (**C**) Alaska site with FluoSpec 2; (**D**) FluoSpec 2 in a crop field in Illinois, and (**E**) Nebraska; (**F**) New Mexico. the CCD (Charge-Coupled Device) detector to \(-10\)\({}^{\circ}\)C. During the field measurements, we noticed that cooling down the system below zero Celsius when the relative humidity was high (>80%) caused condensation on the CCD detector. In addition to adding desiccant bags, three solutions were used: (1) before each round of measurement, we pre-heated the instrument to 30 Celsius, which caused the water droplets to evaporate. We then cooled down the instrument back to \(-10\) Celsius for the measurements; (2) the TEC temperature was set to 0 Celsius to increase the dark current but eliminate the condensation. We found that the differences in the level of dark current were small--between \(-10\) Celsius and 0 Celsius (see next section); and (3) an additional water tight enclosure was added to protect the QEpro spectrometer. Several methods were adopted to increase the signal received by the spectrometer. First, the size of the fiber optics was increased from 600 \(\upmu\)m to 1000 \(\upmu\)m. Second, at the FOS 2 \(\times\) 2 shutter, the focus of the fibers on each end of the port was adjusted to increase the light intensity. After these adjustments, the integration time for the bare fiber side facing vegetation to reach a digital number around 100,000 was around 0.8 s on a sunny day and 1.3-2 s for the cosine corrector that faces the sky. Cosine correctors, like other diffusers, cause significant signal loss and require a longer integration time. It should be noted that certain types of cosine corrector do not have a perfect cosine response, particularly when the incident angle from the sun is low, causing erroneous SIF retrievals when oxygen bands approaches are used (data not shown).