zooplankton | R Documentation |
Various features measured by image analysis with the package zooimage
and
ImageJ
on samples of zooplankton originating from Tulear, Madagascar. The
taxonomic classification is also provided in the class
variable.
zooplankton
A data frame with 19 variables:
ecd
The "equivalent circular diameter", the diameter of a circle with the same area as the particle (in mm).
area
The area of the particle on the image (in mm^2).
perimeter
The perimeter of the particle (in mm).
feret
The Feret diameter, that is, the largest measured diameter of the particle on the image (mm).
major
The major axis of the ellipsoid matching the particle (mm).
minor
The minor axis of the same ellipsoid (mm).
mean
The mean value of the gray levels calibrated in optical density (OD), thus, unitless.
mode
The most frequent gray level in that particle in OD.
min
The most transparent part in OD.
max
The most opaque part in OD.
std_dev
The standard deviation of the OD distribution inside the particle.
range
Transparency range as max
- min
.
size
The mean diameter of the particle, as the average of
minor
and major
(mm).
aspect
Aspect ratio of the particle as minor
/major
.
elongation
The area
divided by the area of a circle of the
same perimeter
of the particle.
compactness
sqrt((4/pi) * area
) / major
.
transparency
1 - (ecd
- size
).
circularity
4pi(area
/ perimeter
^2).
density
Density integrate by the surface covered by each gray level, i.e. O.D., inside the particle.
class
The classification of this particle. 17 classes are made.
Note that Copepods
are Calanoid
+ Cyclopoid
+ Harpactivoid
+
Poecilostomatoid
and they represent the most abundant zooplankton at sea.
This is a typical training set used to train a plankton classifier with machine learning algorithms. Organisms originate from various samples (different seasons, depth, etc. to take the variability into account). However, the abundance of the different classes do not match abundance found in each sample, i.e., rare classes are over-represented in this training set. Only zooplankton classes are present in the dataset. Full data also contains classes for phytoplankton, marine snow, etc. Take care that several variables are correlated!
Grosjean, Ph & K. Denis (2004). Supervised classification of images, applied to plankton samples using R and ZooImage. Chap.12 of Data Mining Applications with R. Zhao, Y. & Y. Cen (eds). Elsevier. Pp 331-365. https://doi.org/10.1016/C2012-0-00333-X.
table(zooplankton$class)
library(ggplot2)
ggplot(zooplankton, aes(circularity, transparency, color = class)) +
geom_point()
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