ISIISNet : plankton images captured with the ISIIS (In-situ Ichthyoplankton Imaging System)

Plankton was imaged with an In Situ Ichthyoplankton Imaging System, between surface and ~100m, over 10 days in July 2016, in the North Western Mediterranean Sea. This deployment was the core of the VISUFRONT cruise. The image generated by the linescan, shadowgraph camera of ISIIS were processed with the custom software apeep and regions of interest, targeted to be planktonic organisms by a deep segmenter, were extracted. The 408,166 resulting objects were sorted by a limited number of operators, following a common taxonomic guide, into 32 taxa, using the web application EcoTaxa http://ecotaxa.obs-vlfr.fr. For the purpose of training machine learning classifiers, the images in each class were split into training, validation, and test sets, with proportions 70%, 15% and 15%.

The archive contains :

taxa.csv.gz

Table of the classification of each object in the dataset, with columns :

  • objid: id of the object (in Ecotaxa)
  • taxon_level1: name of the taxon corresponding to the level 1 classification
  • lineage_level1: taxonomic lineage corresponding to the level 1 classification
  • taxon_level2: name of the taxon corresponding to the level 2 classification
  • plankton: indicates if the object is a plankton (boolean)
  • set: class of the image corresponding to the taxon (train : training, val : validation, or test)
  • img_path: local path of the image corresponding to the taxon (of level 1), named according to the object id

features_native.csv.gz

Table of morphological features recomputed with skimage.measure.regionprops on the ROIs produced by software. See http://scikit-image.org/docs/dev/api/skimage.measure.html#skimage.measure.regionprops for documentation.

inventory.tsv

Tree view of the taxonomy and number of images in each taxon, displayed as text. With columns :

  • lineage_level1: taxonomic lineage corresponding to the level 1 classification
  • taxon_level1: name of the taxon corresponding to the level 1 classification
  • n: number of objects in each taxon class 

map.png

Map of the sampling locations, to give an idea of the diversity sampled in this dataset.

imgs

Directory containing images of each object, named according to the object id objid and sorted in subdirectories according to their taxon.

Disciplines

Biological oceanography

Keywords

plankton, image, ISIIS

Location

43.69N, 43.29S, 7.79E, 7.32W

Devices

ISIIS:

Cowen RK, Guigand CM (2008) In situ Ichthyoplankton Imaging System (ISIIS): system design and preliminary results. Limnology and Oceanography: Methods 6:126–132.

Processing software:

https://github.com/jiho/apeep

Data

FileSizeFormatProcessingAccess
ISIISNet
758 MotarProcessed data
How to cite
Panaïotis Thelma, Caray-Counil Louis, Jalabert Laetitia, Irisson Jean-Olivier (2024). ISIISNet : plankton images captured with the ISIIS (In-situ Ichthyoplankton Imaging System). SEANOE. https://doi.org/10.17882/101950

Copy this text