Dutta, SomnathPavoni, GaiaCorsini, MassimilianoGanovelli, FabioCignoni, PaoloRossi, PaoloCenni, ElenaSimonini, RobertoGrassi, FrancescaCassanelli, DavideCattini, StefanoRovati, LuigiCapra, AlessandroCastagnetti, CristinaGünther, TobiasMontazeri, Zahra2025-05-092025-05-092025978-3-03868-269-11017-4656https://doi.org/10.2312/egp.20251022https://diglib.eg.org/handle/10.2312/egp20251022We present an automated framework for counting and measuring the polyps of Cladocora caespitosa, a Mediterranean reefbuilding coral. To our knowledge, the most practical method for counting polyps currently involves ecologists' visual inspection of a 3D model. However, measuring polyps from the model can lead to inaccuracies due to distortions in the reconstruction. Our method integrates deep learning-based instance segmentation on 2D images with 3D models for unique polyp identification, ensuring precise biometric extraction. The proposed pipeline automates polyp detection, counting, and measurement while overcoming the limitations of manual in situ methods. Laboratory validation demonstrates its accuracy and efficiency, paving the way for scalable, high-resolution phenotyping, and field monitoring of Mediterranean coral populations.Attribution 4.0 International LicenseCCS Concepts: Computing methodologies → Object recognition; Image segmentation; Shape analysisComputing methodologies → Object recognitionImage segmentationShape analysis10.2312/egp.202510222 pages