patternize: An R package for quantifying colour pattern variation

Methods in Ecology and Evolution
Steven M Van BelleghemBrian A Counterman

Abstract

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...Continue Reading

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Citations

May 10, 2019·Journal of Evolutionary Biology·Marcela Méndez-JanovitzConstantino Macías Garcia
Mar 12, 2020·Molecular Ecology·James D BurgonKathryn R Elmer
May 7, 2020·Proceedings. Biological Sciences·M F González-RojasC Salazar
Jul 23, 2020·Proceedings. Biological Sciences·Steven M Van BelleghemRiccardo Papa
Sep 18, 2020·Journal of Evolutionary Biology·Hannah E BainbridgeNicola J Nadeau
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Dec 4, 2020·Science Advances·Seita Miyazawa
Feb 19, 2021·Evolution; International Journal of Organic Evolution·Christopher R HemingsonDavid R Bellwood
Aug 23, 2019·Developmental Biology·Nicolas Haupaix, Marie Manceau
Mar 2, 2019·Trends in Genetics : TIG·Pauline SalisBruno Frédérich
Jul 6, 2021·Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics·Liming ChangJianping Jiang

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