PELGAS Bay of Biscay ZooScan zooplankton Dataset (2004-2016)

This dataset is composed of 1,153,507 zooplankton individuals, zooplankton parts, non-living particles and imaging artefacts, ranging from 300 µm to 3.39 mm Equivalent Spherical Diameter, individually imaged and measured with the ZooScan (Gorsky et al., 2010). The objects were sorted in 127 taxonomic and morphological groups. The imaged objects originate from samples collected on the Bay of Biscay continental shelf, in spring, from 2004 to 2016 during the PELGAS ecosystemic surveys (Doray et al., 2018). The samples were collected with a WP2 200 µm mesh size fitted with a Hydrobios (back-run stop) mechanical flowmeter, generally from 100 m depth to the surface, or 5 m above the sea floor (if bottom depth less than 100 m) in vertical hauls, at night. From 2004 to 2006, vertical WP2 net tows were performed in the anchovy core distribution area in the southern Bay of Biscay and North of it until the Loire estuary only. Since 2009, WP2 sampling has been carried out at all PELGAS stations, up to the southern coast of Brittany. The samples were preserved in 4% buffered formaldehyde seawater solution directly after collection, until 2019-2020 where they were imaged with the ZooScan, in the lab, on land. Each imaged object is geolocated, associated to a station, a cruise, a year and other metadata that enable the reconstruction of quantitative zooplankton communities for ecological studies (i.e. Grandrémy et al., 2023a). Each object is described by 46 morphological and grey level based features (8 bits encoding, 0 = black, 255 = white), including size, automatically extracted on each individual image by the Zooprocess. Each object was taxonomically identified using the web based application Ecotaxa with built-in, random forest and CNN based, semi-automatic sorting tools followed by expert validation or correction (Picheral et al., 2017). This dataset is intended to be used for ecological studies as well as machine learning applied to plankton studies. The archive contains: - One tab separated file (PELGAS ZooScan zooplankton dataset) containing all data and metadata associated to each imaged and identified object. Metadata and features are in columns (n =71) and objects are in rows (n = 1,153,507). - One comma separated file containing the name, type, definition and unit of each field (column) in the .tsv (dataset_descriptor_zooscan). - One comma separated file containing the taxonomic list of the dataset, with counts and nature of the content of the category, i.e. “T” for taxonomical category, and “M” for morphological category (taxonomy_descriptor_zooscan). - A individual_images directory containing images of each imaged object sorted in subdirectories named according to objects’ identifications object_taxon appended to an Ecotaxa internal taxon numerical id classif_id (i.e. taxon__123456789) across years and sampling stations. Within subdirectories, each object is named after its unique internal Ecotaxa identifier, objid. - A Map of the sampling station location over the 2004-2016 period

本数据集共包含1,153,507个浮游动物个体、浮游动物残体、非生物颗粒物及成像伪影，等效球直径范围为300微米至3.39毫米，所有样本均通过ZooScan设备（ZooScan）完成单一个体的成像与尺寸测量（Gorsky等，2010）。所有研究对象被划分为127个分类学与形态学群组。所有成像样本均来自2004年至2016年春季于比斯开湾（Bay of Biscay）大陆架开展的PELGAS生态系统调查（Doray等，2018）所采集的样品。
样品采用配备Hydrobios逆流止回机械流量计的WP2型200微米网孔网具采集，通常采用垂直拖网方式于夜间采样：采样深度一般为从100米水深至表层；若海底水深小于100米，则采样深度为海底上方5米处。2004年至2006年期间，垂直WP2网拖采样仅在比斯开湾南部鳀鱼核心分布区及其以北至卢瓦尔河河口区域开展。2009年起，WP2采样覆盖所有PELGAS调查站位，直至布列塔尼南部海岸。
样品采集后立即保存于4%缓冲甲醛海水溶液中，直至2019-2020年在实验室陆地环境中通过ZooScan完成成像。每个成像对象均附带地理位置信息，关联至对应站位、航次、年份及其他元数据（metadata），可用于重建定量浮游动物群落以支持生态学研究（Grandrémy等，2023a）。
每个对象由Zooprocess工具（Zooprocess）自动从单张图像中提取46项基于形态学与灰度级的特征（采用8位编码，0代表黑色，255代表白色），其中包含尺寸信息。所有对象均通过基于网页的应用程序Ecotaxa（Ecotaxa）完成分类学鉴定，该工具内置随机森林（random forest）与基于卷积神经网络（Convolutional Neural Network，CNN）的半自动分类工具，后续还需经过专家验证或修正（Picheral等，2017）。
本数据集可用于生态学研究以及应用于浮游生物研究的机器学习任务。该归档文件包含以下内容：
- 一个制表符分隔文件（PELGAS ZooScan zooplankton dataset），存储所有与每个成像及鉴定对象相关的数据与元数据。元数据与特征以列形式存储（共71列），每个对象对应一行（共1,153,507行）。
- 一个逗号分隔文件，包含.tsv文件中每个字段（列）的名称、类型、定义与单位（dataset_descriptor_zooscan）。
- 一个逗号分隔文件，包含本数据集的分类学列表，附带各类别的计数与内容性质，其中"T"代表分类学类别，"M"代表形态学类别（taxonomy_descriptor_zooscan）。
- 一个individual_images目录，存储每个成像对象的图像，这些图像按子目录分类，子目录名称根据对象的鉴定结果命名，格式为"分类单元__Ecotaxa内部分类单元数字ID classif_id"（例如taxon__123456789），覆盖所有调查年份与采样站位。在子目录内，每个对象以其唯一的Ecotaxa内部标识符objid命名。
- 一张2004年至2016年期间采样站位的位置分布图