DOI: 10.5281/zenodo.10040995
title: Macroscopic, histological and stereological image dataset of Megrim (Lepidorhombus whiffiagonis) ovaries from the ICES Celtic Seas, south of Greater North sea or Bay of Biscay Ecoregions

description: Contents: 
This dataset contains the macroscopic and histological images of the ovaries of 202 Megrim (female, Lepidorhombus whiffiagonis, Walbaum, 1792) collected from the ICES Celtic Seas, south Greater North sea or Bay of Biscay Ecoregions (Eco) in November 2019 (n=25; Eco=7h & 7j), November 2020 (n=14, Eco=7h & 7j), December 2020 (n=1, Eco=7h), May 2021 (n=15, Eco=7h & 7g), June 2021 (n=15, Eco=7h), July 2021 (n=15, Eco=7h & 7e), October 2021 (n=15, Eco=7g & 7f), October 2021 (n=6, Eco=8a & 8b & 8c), November 2021 (n=6, Eco=8a & 8b), November 2021 (n=15, Eco=7j), December 2021 (n=15, Eco=7e & 7g), January 2022 (n=15, Eco=7f), February 2022 (n=15, Eco=7g), March 2022 (n=15, Eco=7g) and May 2022 (n=15, Eco=7g).
 
Images:

Macroscopic_pictures.zip: archive in zip format of 549 pictures (.JPG; 2Mo-8Mo; JPG; 350pp) from 202 female megrim 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 et al., 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.
Histology_slides.zip : archive in zip format containing the ovarian histological slides digitized using an Aperio CS (Scan Scope Console software, v.10.2.0.2352), x20 lens. The whole slide images (.svs) are of the 461 histological slides acquired during this study. 
 
Data:

Readings.zip : archive in zip format containing the stereology reading results of the ovarian histological slides. In this folder, three directories are available. 

Calibration : Reading results of 3 different agents, with the first and last readings, as well as the QuPath scripts used.
Homogeneity : Reading results for 102 histological slides used to check the cellular homogeneity inter- and intra-gonad. These 102 slides belong to 17 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.
Total : Reading results for 202 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.
Macro_WHI_read_me.txt : a text file (.txt) listing the acronyms used in the Macro_WHI.xlsx file, as well as their meaning.
Macro_WHI.xlsx : Excel file (.xlsx) containing measurements of macroscopic parameters for all 202 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 (Macroscopic_pictures_Data)
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 et al., 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
Stereo_MULL_read_me.txt : a text file (.txt) listing the acronyms used in the Stereo_MULL.csv file, as well as their meaning.
Stereo_MULL.csv : a text data file (.csv) of the stereology count results of 287 slides read during this study. Among these slides, 102 were read to test the homogeneity distribution of different cell types found throughout each ovary (17 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 Calibration folder for reading results of the 3 agents). Finally, 202 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 et al. 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 Fish_id
 
Contact :
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 any enquiries, please contact: carine.sauger@gmail.com or laurent.dubroca@ifremer.fr