## 2 Materials and Methods
### Software, Operation, and Data Collection and Management Design  
We developed custom software to operate the EcoSpec system in a Linux environment, including collection of hyperspectral EMR measurements. The software package allows a range of autonomous functions for the system, which include (1) initiating the system 20 min before sunrise each day, (2) triggering activities of the components in a synchronized manner, (3) monitoring system functions and sending an email alert when malfunction is detected, (4) rebooting the system when malfunction is detected, (5) transmitting the data approximately every 30 min throughout the day, and (6) shutting down the system at sunset each day.  
The system automatically initiates 20 min before sunrise each day based on the internal clock with the longitude setting. The PTU rotates 300 degrees (1 full rotation of the system) to test the functionality of the platform and return to position 1. The first spectrometer data collection begins at sunrise at position 1. The actuator extends and places the white reference panel under the fiber optic cable (Video S1). The spectrometer optimizes the parameter setting. Once optimized, the spectrometer collects over 100 white reference measurements from the 99% reflective Spectralon(r) panel and records the average value. The actuator retracts and stores the white panel in the custom housing (Video S1). This protects the surface from elements (e.g., dust) that may impact the integrity of spectral reference measurements. While retracting, the spectrometer measures and records dark current or the sensor's internal noise. Shortly after, the spectrometer collects measurements from the land surface approximately 500 times and records the average value. A RGB photo of the spectrometer FOV and its vicinity is captured during the reflectance measurements from the land surface. Once it completes a full sequence at its current position, the PTU moves to the next position and repeats the series of steps from the spectrometer optimization to land surface measurements before moving on to a subsequent position (Video S1). While rotating 300 degrees for each rotation, the upper package of the system pauses at 12 positions around the tower and collects measurements from the land surface in order to account for local variability within the study site. The data collection sequence continues throughout the day. At sunset, the system moves to position 1 and automatically shuts down to conserve energy for the next day.  
At each position, a set of hyperspectral EMR measurements is comprised of gain, offset, integration time, white reference (2150 features), dark current (2150 features), and land surface measurements (2150 features), and all measurements are temporally recorded in the Raspberry Pi along with measurement identification, PTU position, and sample date and time (Video S1). A set of measurements at a single position typically takes around 1 min. It will take longer when ambient light is low (e.g., cloudy sky conditions, in the early or late day). On a sunny summer day, the system could collect measurements from 800+ data points.  
The system allows us to collect an array of land surface measurements, including hyperspectral reflectance of plants and soils, true-color photos capturing contextual information of land surface, radiant temperature of sky and land, incoming and reflected shortwave radiation, and incoming radiation components (direct and diffuse), as frequently as every minute. Several of the sensors are mounted on a pan-tilt unit on top of the tower to collect hyperspectral reflectance, land surface photos, and radiant temperature of sky and land from 12 discrete positions around the tower. This allows for capturing inherent heterogeneity of the terrestrial ecosystem at a local scale and to obtain representative spectral signatures of the plant and soil surfaces via averaging those measurements.