RT Journal Article
SR Electronic
T1 Patternize: An R package for quantifying color pattern variation
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 121962
DO 10.1101/121962
A1 Steven M. Van Belleghem
A1 Riccardo Papa
A1 Humberto Ortiz-Zuazaga
A1 Frederik Hendrickx
A1 Chris D. Jiggins
A1 W. Owen McMillan
A1 Brian A. Counterman
YR 2017
UL http://biorxiv.org/content/early/2017/03/29/121962.abstract
AB The use of image data to quantify, study and compare variation in the colors and patterns of organisms requires the alignment of images to establish homology, followed by color-based segmentation of images. Here we describe an R package for image alignment and segmentation that has applications to quantify color patterns in a wide range of organisms.patternize is an R package that quantifies variation in color patterns obtained from image data. patternize first defines homology between pattern positions across specimens either through fixed landmarks or automated image registration. Pattern identification is performed by categorizing the distribution of colors using either an RGB threshold or unsupervised image segmentation.We demonstrate that patternize can be used for quantification of the color patterns in a variety of organisms by analyzing image data for butterflies, guppies and spiders. Image data can be compared between sets of specimens, visualized as heatmaps and analyzed using principal component analysis (PCA).patternize has potential applications for fine scale quantification of color pattern phenotypes in population comparisons, genetic association studies and investigating the genetic basis of color pattern expression across a wide range of organisms.