Automatic method to transform routine otolith images for a standardized otolith database using R.

• Main Authors: Andrialovanirina, Nicolas, Hache, Alizée, Mahé, Kélig, Couette, Sébastien, Poisson Caillault, Émilie
• Other Authors: Laboratoire Ressources Halieutiques La Rochelle-L'Houmeau ( LRHLR), Unité Halieutique Gascogne Sud (HGS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire d'Informatique Signal et Image de la Côte d'Opale (LISIC), Université du Littoral Côte d'Opale (ULCO), Biogéosciences UMR 6282 (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), École Pratique des Hautes Études (EPHE), Université Paris Sciences et Lettres (PSL), Study supported by the Data Collection Framework (DCF; EC Reg. 199/2008, 665/2008; Decisions 2008/949/EC and2010/93/EU), by the Institut Français de Recherche et d’Exploitation de la Mer and the ULCO University (doctoral support to N. ANDRIALOVANIRINA, 2021-2024)., ANR-21-EXES-0011,IFSEA,Transdisciplinary graduate school for marIne, Fisheries and SEAfood sciences(2021)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2023
• Subjects: Binarization; Image processing; Otoliths; Rotation; Shape analysis; Standardization; [SDE.BE]Environmental Sciences/Biodiversity and Ecology; Arctic cod; Arctic; Gadus morhua
• Online Access: https://u-bourgogne.hal.science/hal-04152498; https://doi.org/10.26028/cybium/2023-471-003

International audience Fisheries management is generally based on age structure models. Thus, fish ageing data are collected by experts who analyze and interpret calcified structures (scales, vertebrae, fin rays, otoliths, etc.) according to a visual process. The otolith, in the inner ear of the fish, is the most commonly used calcified structure because it is metabolically inert and historically one of the first proxies developed. It contains information throughout the whole life of the fish and provides age structure data for stock assessments of all commercial species. The traditional human reading method to determine age is very time-consuming. Automated image analysis can be a low-cost alternative method, however, the first step is the transformation of routinely taken otolith images into standardized images within a database to apply machine learning techniques on the ageing data. Otolith shape, resulting from the synthesis of genetic heritage and environmental effects, is a useful tool to identify stock units, therefore a database of standardized images could be used for this aim. Using the routinely measured otolith data of plaice (Pleuronectes platessa Linnaeus, 1758) and striped red mullet (Mullus surmuletus Linnaeus, 1758) in the eastern English Channel and north-east Arctic cod (Gadus morhua Linnaeus, 1758), a greyscale images matrix was generated from the raw images in different formats. Contour detection was then applied to identify broken otoliths, the orientation of each otolith, and the number of otoliths per image. To finalize this standardization process, all images were resized and binarized. Several mathematical morphology tools were developed from these new images to align and to orient the images, placing the otoliths in the same layout for each image. For this study, we used three databases from two different laboratories using three species (cod, plaice and striped red mullet). This method was approved to these three species and could be applied for others species for age determination ...