Patternize: An R Package For Quantifying Color Pattern Variation
McMillan, W Owen
John Wiley and Sons Inc.
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Van Belleghem, S., Papa, R., Ortiz-Zuazaga, H., Hendrickx, F., Jiggins, C., McMillan, W. O., & Counterman, B. Patternize: An R Package For Quantifying Color Pattern Variation. https://doi.org/10.1101/121962
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 manually placed homologous landmarks or automated image registration. Pattern identification is performed by categorizing the distribution of colors using an RGB threshold, k-means clustering or watershed transformation. 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, spiders and salamanders. 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 basis of color pattern variation across a wide range of organisms.
NSF grant DEB-1257839 NIH grant 5P20GM103475-13
European Research Council (339873)
Isaac Newton Trust (1523(r))
External DOI: https://doi.org/10.1101/121962
This record's URL: https://www.repository.cam.ac.uk/handle/1810/269775