PhenoCam Smart Classifer
The Smart Classifier Algorithm for the "GCE Sapelo" PhenoCam
See: O’Connell, J. L., and M. Alber. 2016. A smart classifier for extracting environmental data from digital image time-series: Applications for PhenoCam data in a tidal salt marsh. Environmental Modelling & Software 84:134–139. http://dx.doi.org/10.1016/j.envsoft.2016.06.025
PhenoCams are part of a national network of automated digital cameras used to assess vegetation phenology transitions. Effectively analyzing PhenoCam time-series involves eliminating scenes with poor solar illumination or high cover of non-target objects such as water. We created a smart classifier to process images from the “GCESapelo” PhenoCam, which photographs a regularly-flooded salt marsh. The smart classifier, written in R, assigns pixels to target (vegetation) and non-target (water, shadows, fog and clouds) classes, allowing automated identification of optimal scenes for evaluating phenology. When compared to hand-classified validation images, the smart classifier identified scenes with optimal vegetation cover with 96% accuracy and other object classes with accuracies ranging from 86 to 100%. Accuracy for estimating object percent cover ranged from 74 to 100%. Pixel-classification with the smart classifier outperformed previous approaches (i.e. indices based on average color content within ROIs) and reduced variance in phenology index time-series. It can be readily adapted for other applications.
You can find a reproducible example to download and run these scripts over on my website: http://conservationecology.weebly.com/projects.html