Improving the Reliability of Scale-Free Image Morphometrics in Applications with Minimally Restrained Livestock Using Projective Geometry and Unsupervised Machine Learning

Advances in neural networks have garnered growing interest in applications of machine vision in livestock management, but simpler landmark-based approaches suitable for small, early stage exploratory studies still represent a critical stepping stone towards these more sophisticated analyses. While such approaches are well-validated for calibrated images, the practical limitations of such imaging systems restrict their applicability in working farm environments. The aim of this study was to validate novel algorithmic approaches to improving the reliability of scale-free image biometrics acquired from uncalibrated images of minimally restrained livestock. Using a database of 551 facial images acquired from 108 dairy cows, we demonstrate that, using a simple geometric projection-based approach to metric extraction, a priori knowledge may be leveraged to produce more intuitive and reliable morphometric measurements than conventional informationally complete Euclidean distance matrix analysis. Where uncontrolled variations in image annotation, camera position, and animal pose could not be fully controlled through the design of morphometrics, we further demonstrate how modern unsupervised machine learning tools may be used to leverage the systematic error structures created by such lurking variables in order to generate bias correction terms that may subsequently be used to improve the reliability of downstream statistical analyses and dimension reduction.