Machine Learning for the Fast and Accurate Assessment of Fitness in Coral Early Life History

As coral reefs continue to degrade globally due to climate change, considerable effort and investment is being put into coral restoration. The production of coral offspring via asexual and sexual reproduction are some of the proposed tools for restoring coral populations and will need to be delivered at scale. Simple, inexpensive, and high-throughput methods are therefore needed for rapid analysis of thousands of coral offspring. Here we develop a machine learning pipeline to rapidly and accurately measure three key indicators of coral juvenile fitness: survival, size, and color. Using machine learning, we classify pixels through an open-source, user-friendly interface to quickly identify and measure coral juveniles on two substrates (field deployed terracotta tiles and experimental, laboratory PVC plastic slides). The method’s ease of use and ability to be trained quickly and accurately using small training sets make it suitable for application with images of species of sexually produced corals without existing datasets. Our results show higher accuracy of survival for slides (94.6% accuracy with five training images) compared to field tiles measured over multiple months (March: 77.5%, June: 91.3%, October: 97.9% accuracy with 100 training images). When using fewer training images, accuracy of area measurements was also higher on slides (7.7% average size difference) compared to tiles (24.2% average size difference for October images). The pipeline was 36× faster than manual measurements. The slide images required fewer training images compared to tiles and we provided cut-off guidelines for training for both substrates. These results highlight the importance and power of incorporating high-throughput methods, substrate choice, image quality, and number of training images for measurement accuracy. This study demonstrates the utility of machine learning tools for scalable ecological studies and conservation practices to facilitate rapid management decisions for reef protection.