Plankton was imaged with Flowcam in contrasted oceanic regions. The full images were processed with the ImageJ software and the regions of interest (ROIs) around each individual object were recorded. A set of associated features were measured on the objects. All objects were classified by a limited number of operators into 167 different classes using the web application EcoTaxa (http://ecotaxa.obs-vlfr.fr). The following dataset corresponds to the 301, 247 objects and their calculated features. The different files provide information about the features of the objects, their taxonomic identification as well as the raw images.

The archive contains :

taxa.csv.gz

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

• objid: unique object identifier in EcoTaxa (integer number).
• taxon_level1: taxonomic name 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

• objid: unique object identifier in EcoTaxa (integer number).
• area: surface area of the object (integer number)
• mean: average grey value within the object; sum of the grey values of all pixels in the object divided by the number of pixels
• stddev: standard deviation of the grey value used to generate the mean grey value
• mode: modal grey value within the object
• min: minimum grey value within the object (0 = black)
• max: maximum grey value within the object (255 = white)
• perim: the length of the outside boundary of the object
• width: width of the smallest rectangle enclosing the object
• height: height of the smallest rectangle enclosing the object
• major: primary axis of the best fitting ellipse for the object
• minor: secondary axis of the best fitting ellipse for the object
• angle: angle between the primary axis and a line parallel to the x-axis of the image
• circ: circularity = (4 * Pi * Area) / Perim2) ; a value of 1 indicates a perfect circle, a value approaching 0 indicates an increasingly elongated polygon
• feret: maximum feret diameter, i.e., the longest distance between any two points along the object boundary
• intden: integrated density. This is the sum of the grey values of the pixels in the object (i.e. = Area*Mean)
• median: median grey value within the object
• skew: skewness of the histogram of grey level values
• kurt: kurtosis of the histogram of grey level values
• %area: percentage of object’s surface area that is comprised of holes, defined as the background grey level
• area_exc: surface area of the holes in the object, in square pixels (=Area*(1-(%area/100))
• fractal: fractal dimension of object boundary (Berube and Jebrak 1999)
• skelarea: surface area of skeleton in pixels. In a binary image, skeleton is obtained by repeatedly removing pixels from the edges of objects until they are reduced to the width of a single pixel
• slope: slope of the grey level normalized cumulative histogram
• histcum1, 2, 3: grey level value at the first, second and third quartile of the normalized cumulative histogram of grey levels
• nb1 nb2 nb3: number of remaining objects in the image after thresholding on level Histcum1, 2 and 3
• symetrieh: bilateral horizontal symmetry index
• symetriev: bilateral vertical symmetry index
• symetriehc: symmetry of the largest remaining object in relation to the horizontal axis after thresholding at the grey level Histcum1 value
• symetrievc: symmetry of the largest remaining object in relation to the vertical axis after thresholding at the grey level Histcum1 value
• convperim: the perimeter of the smallest polygon within which all points in the object fit
• convarea: the area of the smallest polygon within which all points in the object fit
• fcons: measure of contrast based in the texture feature descriptor (Amadasun and King, 1989)
• thickr: thickness ratio : relation between the maximum thickness of an object and the averag thickness of the object excluding the maximum
• esd: equivalent spherical diameter
• elongation: major / minor
• range: max - min
• meanpos: (mean-max) / (mean-min)
• cv: 100*(stddev/mean)
• sr: 100*(stddev/(max-min))
• perimferet: perim/feret
• perimmajor: perim/major
• circex: (4*PI*area_exc)/(pow(perim,2))

features_skimage.csv.gz

Table of morphological features recomputed with skimage.measure.regionprops on the ROIs produced by ZooCAM. 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 group

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.