Estimating Conformational Traits in Dairy Cattle With DeepAPS: A Two-Step Deep Learning Automated Phenotyping and Segmentation Approach

Assessing conformation features in an accurate and rapid manner remains a challenge in the dairy industry. While recent developments in computer vision has greatly improved automated background removal, these methods have not been fully translated to biological studies. Here, we present a composite method (DeepAPS) that combines two readily available algorithms in order to create a precise mask for an animal image. This method performs accurately when compared with manual classification of proportion of coat color with an adjusted R(2) = 0.926. Using the output mask, we are able to automatically extract useful phenotypic information for 14 additional morphological features. Using pedigree and image information from a web catalog (www.semex.com), we estimated high heritabilities (ranging from h(2) = 0.18–0.82), indicating that meaningful biological information has been extracted automatically from imaging data. This method can be applied to other datasets and requires only a minimal number of image annotations (∼50) to train this partially supervised machine-learning approach. DeepAPS allows for the rapid and accurate quantification of multiple phenotypic measurements while minimizing study cost. The pipeline is available at https://github.com/lauzingaretti/deepaps.