The various facets of digital repeat photography fully exploited with the phenopix R package

Flux towers are more and more often equipped with digital cameras (aka phenocams) widely used to track canopy greenness. Phenocam-derived vegetation indices can capture land surface phenology but also seasonality in gross primary production (GPP) estimated from eddy covariance (EC) measurements. In addition, phenocams can be used to track seasonal development of different species or individuals within the same image scene, and evaluate spatial variability within the footprint of EC measurements. Further, phenocams were recently used to quantify disturbance such as late frost, fires, storms etc. in forested ecosystems and the impact of climate extremes on ecosystem functioning. With the recent rapid development of phenocameras, the need for up-to-date, efficient, open-source software is also increasing tremendously. The phenopix R package was developed for this purpose. In this contribution, we will provide an overview of the software capabilities, with a special focus on how EC measurements can benefit from phenocam data streams.

The steps of a basic processing workflow will be illustrated, including drawing a region of interest (ROI) on an image; extracting red, green and blue digital numbers from a seasonal series of images; depicting greenness index trajectories; fitting a curve to the seasonal trajectories; extracting relevant phenological thresholds (phenophases); characterizing phenophase uncertainties. A focus will be made on recent software developments, including the calculation of camera-derived NDVI and other infrared-based indices, and the handling of shifts in the field of view of the phenocameras.