Macroscopic and histological image dataset of the European plaice (Pleuronectes platessa) ovaries

Macroscopic and histological image dataset of the European plaice (Pleuronectes platessa) ovaries 

Authors:

Carine Sauger¹, Jérôme Quinquis¹, Kristell Kellner², Clothilde Heude-Berthelin², Mélanie Lepoittevin², Nicolas Elie³, Laurent Dubroca¹

Affiliations:

1 : Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER). Laboratoire Ressources Halieutiques de Port-en-Bessin, Avenue du Général de Gaulle, 14520, Port-en-Bessin-Huppain, Calvados

2 : Biologie des Organismes et Ecosystèmes Aquatiques (FRE 2030 BOREA). Université de Caen Normandie, Esplanade de la Paix, CS 14032, Caen, Calvados

3 : Centre de Microscopie Appliquée à la Biologie (SF 4206 ICORE, CMABIO3). Université de Caen Normandie, Esplanade de la Paix, CS 14032, Caen, Calvados

Contents: This dataset was established during a 6 month long Master’s degree internship (February to July 2019), under the IFREMER (Institut Français de Recherche pour l'Exploitation de la Mer) project MATO (MATurité Objective des poissons par l’histologie quantitative), with the collaboration of two research facilities from the University of Caen-Normandie : BOREA (Biologie des Organismes et Ecosystèmes Aquatiques) and CMABIO3 (Centre de Microscopie Appliquée à la Biologie).

This dataset contains the macroscopic and the histological images of the ovaries of 151 European plaices (female, Pleuronectes platessa) collected along the French Coast of the English Channel (ICES area 27.7.d) in 2017, 2018 and 2019.

Images:

• Full_Ovaries_Data.zip: archive in zip format of 151 pictures (.JPG; 8Mo-9Mo; sRGB; 6016x4000 pixels) of both ovaries from 151 female plaice dissected during this study. Each photo was taken by the same person with a Nikon camera (D3200), in the same room with identical lightening methods (no flash). For each picture, both ovaries were set on a blue background, with a 0.50€ coin for size calibration. The upper most ovary is the dorsal gonad of the fish while the lower one is the ventral gonad. The name of the picture is the same as the fish’s ID number.

• Stereology_Readings_Data.zip: archive in zip format of two directories containing the images

• • Interagent_Calibration: the ovarian histological slides were digitized using an Aperio slide scanner (Scan Scope Console software, v.10.2.0.2352, Leica Biosystems), x20 lens. The pictures (.svs: Aperio single-file pyramidal tiled TIFF, with non-standard metadata and compression) are of the 20 histological slides used for the stereological count. 20 slides of 20 fish (with one slide per fish) were analyzed for the intercalibration analysis. The slides used were from the central position of the ventral ovary (V2).

  • Ovary_Slides: the ovarian histological slides were digitized using an Aperio slide scanner (Scan Scope Console software, v.10.2.0.2352, Leica Biosystems), x20 lens. The pictures (Aperio single-file pyramidal tiled TIFF, with non-standard metadata and compression) in this dataset are the 226 histological slides read during this study. With a total of 151 fish dissected, 151 ovarian histological slides of the median position of the ventral ovary were read. Among the remaining slides, 90 were read to analyze the homogeneous distribution of the different cell types. These 90 slides belong to 15 fish, with three histological samples taken in the anterior (1), median (2) and posterior (3) sections of the dorsal (D) and ventral (V) ovaries.

Data frames:

• Intergaent_read_me.txt : a text file (.txt) listing the acronyms used in the Interagent.csv file, as well as their meaning.

• Interagent.csv: a text data file (.csv) with the output of two stereological readings, done by three agents for 15 slides, and by two agents for 20 slides. Between the first and second reading, a reading protocol was set up to help in the determination of the different structures. This protocol allowed the three agents to calibrate themselves with a determination key. This key was necessary for the identification of specific complex structures. The information contained in this table is as follows:

  • agent: code id for the three agents that did the calibration exercise (A, B and C)

  • num_fish: fish number for this study. Here we have 20 different fish

  • fish_id: identification number of the fish. This id number is identical to the name given to the pictures of the full ovaries (Full_Ovaries_Data)

  • scan_id: identification number of the digitized histological slide that was used for the stereological count (Stereology_Readings_Data / Interagent_Calibration)

  • total_points: total number of identified structures for the stereological sampling grid of a slide

  • cell_type: abbreviation of the structure identified (reading protocol available here: https://archimer.ifremer.fr/doc/00501/61235/). In this study, we have 20 different structures

  • hit_points: number of time a structure has been counted on a single slide

  • Fract_estim: percentage (%) of times a structure was counted on a single slide = (100 / total_point) * hit_points

  • reading: reading number. In this study, we have two readings, the first (1) and the second (2)

• Macros_read_me.txt : a text file (.txt) listing the acronyms used in the Macros.csv file, as well as their meaning.

• Macros.csv: a text data file (.csv) containing macroscopic parameters measurements for all 151 fish that have been used during this study. The information contained in this table is as follows:

  • num_fish: fish number for this study. Here we have 151 different female fish

  • fish_id: identification number of the fish. This id number is identical to the name given to the pictures of the full ovaries (Full_Ovaries_Data)

  • gon_pos: gonad position, with D being the dorsal gonad of the individual, and V being the ventral gonad.

  • date: the date the fish was caught (dd/mm/yyyy)

  • L_fish: total length of the fish (cm)

  • W_fish: total weight of the fish (g)

  • mat_estim: visually estimated maturity, after observation of the fish’s gonad with the naked eye, following the WKMATCH (ICES, 2012) scale

  • age: estimated age (in years) of the fish, after analysis of the fish’s otolith. The IFREMER laboratory executed this analysis in Boulogne-sur-Mer (FRANCE)

  • W_gon: gonad weight (g)

  • Kurtosis*: kurtosis parameter

  • Skewness*: skewness coefficient

  • gon_area*: gonad area (mm²)

  • L_gon*: gonad length (mm)

  • width_gon*: maximum gonad width (mm)

  • width_mid_L_gon*: width at mid-length of the gonad (mm)

  • mean_col_index*: the mean color value of the different hues found on the ovary

  • std_dev*: standard deviation of the mean_col_index

  • modal*: modal value or the most frequently occurring color value within the selected ovary

*: values determined after image analysis of the Full_Ovaries_Data with the ImageJ software (v. 1.50J)

• Stereology_read_me.txt : a text file (.txt) listing the acronyms used in the Stereology.csv file, as well as their meaning.

• Stereology.csv: a text data file (.csv) of the stereology count results of 226 slides read during this study. Among these slides, 90 were read to test the homogeneity distribution of different cell types found throughout each ovary (15 fish with 6 histological sections : a median, an anterior and a posterior histological section, for both ovaries), 20 slides were read by two agents for calibration purposes, and 15 of these 20 slides were also read by a third agent for calibration purposes. Finally, 151 median histological slides of the ventral ovary were also read. The information contained in this table is as follows:

  • agent: code id for the 3 agents that did the calibration exercise (A, B and C)

  • num_fish: fish number for this study. Here we have a total of 151 fish

  • fish_id: identification number of the fish. This id number is identical to the name given to the pictures of the full ovaries (Full_Ovaries_Data)

  • scan_id: identification number of the digitized histological slide that was used for the stereological count (Stereology_Readings_Data / Ovary_Slides)

  • reading: reading data to test the homogeneity of cell distributions throughout the ovaries (homogeneity), reading data of the 20 slides read for the inter-agent calibration, and reading data of all the slides (median)

  • cell_type: abbreviation of the structure identified (reading protocol available here: https://archimer.ifremer.fr/doc/00501/61235/). In this study, we have 20 different structures

  • point_id: identification number of the point inside the stereological sampling grid placed over the ovarian histology slide

  • coord_x: x coordinate of the sampling point

  • coord_y: y coordinate of the sampling point

Contact :

For questions, please contact: carine.sauger@gmail.com or laurent.dubroca@ifremer.fr