DOI: 10.5281/zenodo.8060356
title: Macroscopic, histological and stereological image dataset of the Striped red mullet (Mullus surmuletus) ovaries from the English Channel (ICES area 27.7.d) stock

description: <strong>Contents: </strong> This dataset can be completed with the : <strong>Macroscopic, histological and stereological image dataset of the Striped red mullet (<em>Mullus surmuletus</em>) ovaries from the Bay of Biscay (ICES area 27.7.g,j & 27.8.a-c) stock</strong>, which can also be found on the Zenodo repository. This dataset contains the macroscopic and histological images of the ovaries of 214 Striped red mullet (female, <em>Mullus surmuletus</em>, Linnaeus 1758) collected from the English Channel stock (ICES area 27.7.d) in February 2021 (n=20), March 2021 (n=13), April 2021 (n=12), May 2021 (n=15), August 2021 (n=15), September 2021 (n=15), October 2021 (n=41), November 2021 (n=10), December 2021 (n=14), January 2022 (n=30), February 2022 (n=15) and August 2022 (n=14). <strong>Images:</strong> <strong>Macroscopic_pictures.zip: </strong>archive in zip format of 621 pictures (.JPG; 2Mo-8Mo; JPG; 350pp) from 211 female Striped red mullets dissected during this study. Each photo was taken with a digital camera (no flash). For each individual, up to three pictures were taken when possible (Le Meleder <em>et al.</em>, 2022) with : one picture of the entire fish with its abdominal cavity open with the ovaries in view one picture of the whole fish with the ovaries outside of the abdominal cavity one picture of the ovaries the name of the picture is the same as the fish’s ID number. <strong>Histology_slides.zip :</strong> archive in zip format containing the ovarian histological slides digitized using an Olympus V120 slide scanner, x20 lens. The pictures (.vsi from the OlympusVSI format) are of the 484 histological slides acquired during this study. Data was split for smaller size downloads : <strong>Histology_slides_1of5 :</strong> histological sections for individuals numbered 001 to 045 <strong>Histology_slides_2of5 :</strong> histological sections for individuals numbered 046 to 138 <strong>Histology_slides_3of5 :</strong> histological sections for individuals numbered 154 to 180 <strong>Histology_slides_4of5 :</strong> histological sections for individuals numbered 196 to 270 <strong>Histology_slides_5of5 :</strong> histological sections for individuals numbered 271 to 334 <strong>Data:</strong> <strong>Readings.zip :</strong> archive in zip format containing the stereology reading results of the ovarian histological slides. In this folder, three directories are available. <strong>Calibration</strong> : Reading results of 4 different agents, with the first and last readings, as well as the Qupath scripts used. <strong>Homogeneity</strong> : Reading results for 96 histological slides used to check the cellular homogeneity inter- and intra-gonad. These 96 slides belong to 16 fish, with three histological samples taken in the anterior (1), median (2) and posterior (3) sections of the left (G) and right (D) ovaries. A QuPath folder is also present, containing the scripts used. <strong>Total </strong>: Reading results for 214 ovarian histological slides of the median position of either the left or right ovary. One median slide was read per sampled fish. A QuPath folder is also present, containing the scripts used. <strong>Macro_MULL_read_me.txt</strong> : a text file (.txt) listing the acronyms used in the <strong>Macro_MULL.xlsx</strong> file, as well as their meaning. <strong>Macro_MULL.xlsx</strong> : Excel file (.xlsx) containing measurements of macroscopic parameters for all 214 fish sampled during this study. The information contained in this table is as follows: Fish_id: identification of the fish. This id is identical to the name given to the pictures of the full ovaries (<strong>Macroscopic_pictures_Data</strong>) ICES _Division: International Council for the Exploration of the Sea (ICES) division where the fish was sampled in the Food and agricultural Organization of the United nations (FAO) fishing area 27 ICES_statistical_rectangle : Statistical rectangle where the fish was sampled within the FAO fishing area 27 Date: date the fish was caught (dd/mm/yyyy) Total_fish_length: total length of the fish (cm) Ungutted_fish_weight: total weight of the fish (g) Otolith_ID: unique identification number given to each sampled fish through the Imagine (Ellebode <em>et al.</em>, 2022) software used by IFREMER Parasite: presence (Y) or absence (N) of parasite in or on the fish age: age (in years) of the fish after analysis of the fish’s otolith. The IFREMER laboratory of Boulogne-sur-Mer (FRANCE) executed this analysis Visual_maturity : visually estimated maturity, after observation macroscopic criteria of the fish’s gonad with the naked eye, following the WKASMSF (ICES, 2018) scale Liver_weight: liver weight (g) Droite_gonad_weight : gonad weight (g) of right ovary Gauche_gonad_weight : gonad weight (g) of left ovary Sections: number of cross sections sampled for the individual <strong>Stereo_MULL_read_me.txt</strong> : a text file (.txt) listing the acronyms used in the <strong>Stereo_MULL.csv</strong> file, as well as their meaning. <strong>Stereo_MULL.csv</strong> : a text data file (.csv) of the stereology count results of 294 slides read during this study. Among these slides, 96 were read to test the homogeneity distribution of different cell types found throughout each ovary (16 fish with 6 histological sections : a median, an anterior and a posterior histological section, for both ovaries), slides were read by multiple agents for calibration purposes (see <strong>Calibration</strong> folder for reading results of the 4 agents). Finally, 214 median histological ovarian slides were read. The information contained in this table is as follows: cell_type: structure identified for one sample point (for the abbreviations, see Heude-Berthelin <em>et al.</em> 2023) idpt: identification number of the sampling point id: unique complex identification number of the sampling point generated by combining the x and y coordinates x: x coordinate of the sampling point y: y coordinate of the sampling point reading: Indicates if the reading data was used to test cellular homogeneity (Homogeneity) or to the sexual maturity phase slideid: identification number of the digitized histological slide that was used for the stereological count. Shares the same 12 first characters with <strong>Fish_id</strong>
description: This dataset was established under the MATO (MATurité Objectif des poissons par l'histologie quantitative) project, during the PhD of Carine Sauger (October 2021-2023), financed by France Fillière Pêche (FFP/2020/AM/MF/109), under the supervision of IFREMER (Institut Français de Recherche pour l'Exploitation de la Mer) and BOREA (Biologie des Organismes et Ecosystèmes Aquatiques), and with the collaboration of a research facility from the University of Caen-Normandie : CMABIO3 (Centre de Microscopie Appliquée à la Biologie). For questions please contact: carine.sauger@gmail.com or laurent.dubroca@ifremer.fr
description: {"references": ["Dubroca Laurent, Elie Nicolas, Heude-Berthelin Clothilde, Kellner Kristell, Le Meleder Anna, Lepoittevin M\u00e9lanie, Martin Valentine, Nivet Timothe, Sauger Carine, Villain-Naud Nad\u00e8ge (2023). Stereology reading protocol when using quantitative histology for the determination of sexual maturity in fish ovaries. https://doi.org/10.13155/75173", "Elleboode Romain, Badts Vincent, Prigent Glenn, Aumond Yoann, Dussuel Antoine (2022). Guide d'utilisation de l'ex\u00e9cutable QrCodeGenerator. https://doi.org/10.13155/86231", "ICES (2018). Report of the Workshop for Advancing Sexual Maturity Staging in Fish (WKASMSF) 30 April - 4 May 2018, Copenhagen, Denmark. ICES CM/EOSG:38.", "Le Meleder Anna, Sauger Carine, Dubroca Laurent (2022). Protocole de photographie des gonades de poisson / Fish gonads' photography protocol. RBE-HMMN-LRHPB. https://doi.org/10.13155/89703"]}