Quantification of Color Pattern Variation

Quantification of variation in organismal color patterns as obtained from image data. Patternize defines homology between pattern positions across images either through fixed landmarks or image registration. Pattern identification is performed by categorizing the distribution of colors using RGB thresholds or image segmentation.


Quantifying variation in color patterns to study and compare the consistency of their expression necessitates the homologous alignment and color-based segmentation of images. Patternize is an R package that quantifies variation in color patterns as obtained from image data. Patternize defines homology between pattern positions across specimens either through fixed landmarks or image registration. Pattern identification is performed by categorizing the distribution of colors using either an RGB threshold or an unsupervised image segmentation. The quantification of the color patterns can be visualized as heat maps and compared between sets of samples.

Install patternize in R from CRAN:

install.packages("patternize")

Install patternize in R from GitHub using devtools:

install.packages("devtools")
library(devtools)
install_github("StevenVB12/patternize")
# Morpho has commited a change that affects computeTransform used in
# the patternize functions patLanRGB and patLanK (not available in CRAN)
install_github("zarquon42b/Morpho")

For examples see package examples or https://github.com/StevenVB12/patternize-examples

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Reference manual

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install.packages("patternize")

0.0.2 by Steven Van Belleghem, 3 months ago


https://github.com/StevenVB12/patternize


Report a bug at https://github.com/StevenVB12/patternize/issues


Browse source code at https://github.com/cran/patternize


Authors: Steven Van Belleghem [aut, cre]


Documentation:   PDF Manual  


GPL-3 license


Imports raster, sp, rgdal, abind, Morpho, dplyr, imager, magrittr, purrr, vegan, RNiftyReg


See at CRAN