Revisiting giraffe photo-identification using deep learning and network analysis

Abstract

An increasing number of ecological monitoring programs rely on photographic capture-recapture of individuals to study distribution, demography and abundance of species. Photo-identification of individuals can sometimes be done using idiosyncratic coat or skin patterns, instead of using tags or loggers. However, when performed manually, the task of going through photographs is tedious and rapidly becomes too time consuming as the number of pictures grows. Computer vision techniques are an appealing and unavoidable help to tackle this apparently simple task in the big-data era. In this context, we propose to revisit animal re-identification using image similarity networks and metric learning with convolutional neural networks (CNNs), taking the giraffe as a working example. We first developed an end-to-end pipeline to retrieve a comprehensive set of re-identified giraffes from about 4, 000 raw photographs. To do so, we combined CNN-based object detection, SIFT pattern matching, and image similarity networks. We then quantified the performance of deep metric learning to retrieve the identity of known individuals and detect unknown individuals never seen in the previous years of monitoring. After a data augmentation procedure, the re-identification performance of the CNN reached a Top-1 accuracy of about 90%, despite the very small number of images per individual in the training data set. While the complete pipeline succeeded in re-identifying known individuals, it slightly under-performed with unknown individuals. Fully based on open-source software packages, our work paves the way for further attempts to build automatic pipelines for re-identification of individual animals, not only in giraffes but also in other species.