A semi-automatic workflow to process images from small mammal camera traps

Abstract

Camera traps have become popular for monitoring biodiversity, but the huge amounts of image data that arise from camera trap monitoring represent a challenge and artificial intelligence is increasingly used to automatically classify large image data sets. However, it is still challenging to combine automatic classification with other steps and tools needed for efficient, quality-assured and adaptive processing of camera trap images in long-term monitoring programs. Here we propose a semi-automatic workflow to process images from small mammal cameras that combines all necessary steps from downloading camera trap images in the field to a quality checked data set ready to be used in ecological analyses. The workflow is implemented in R and includes (1) managing raw images, (2) automatic image classification, (3) quality check of automatic image labels, as well as the possibilities to (4) retrain the model with new images and to (5) manually review subsets of images to correct image labels. We illustrate the application of this workflow for the development of a new monitoring program of an Arctic small mammal community. We first trained a classification model for the specific small mammal community based on images from an initial set of camera traps. As the monitoring program evolved, the classification model was retrained with a small subset of images from new camera traps. This case study highlights the importance of model retraining in adaptive monitoring programs based on camera traps as this step in the workflow increases model performance and substantially decreases the total time needed for manually reviewing images and correcting image labels. We provide all R scripts to make the workflow accessible to other ecologists