Hyperspectral imaging in animal coloration research: A user-friendly pipeline for image generation, analysis, and integration with 3D modeling

Hyperspectral imaging—a technique that combines the high spectral resolution of spectrophotometry with the high spatial resolution of photography—holds great promise for the study of animal coloration. However, applications of hyperspectral imaging to questions about the ecology and evolution of animal color remain relatively rare. The approach can be expensive and unwieldy, and we lack user-friendly pipelines for capturing and analyzing hyperspectral data in the context of animal color. Fortunately, costs are decreasing and hyperspectral imagers are improving, particularly in their sensitivity to wavelengths (including ultraviolet) visible to diverse animal species. To highlight the potential of hyperspectral imaging for animal coloration studies, we developed a pipeline for capturing, sampling, and analyzing hyperspectral data (here, in the 325 nm to 700 nm range) using avian museum specimens. Specifically, we used the pipeline to characterize the plumage colors of the King bird-of-paradise (Cicinnurus regius), Magnificent bird-of-paradise (C. magnificus), and their putative hybrid, the King of Holland’s bird-of-paradise (C. magnificus x C. regius). We also combined hyperspectral data with 3D digital models to supplement hyperspectral images of each specimen with 3D shape information. Using visual system-independent methods, we found that many plumage patches on the hybrid King of Holland’s bird-of-paradise are—to varying degrees—intermediate relative to those of the parent species. This was true of both pigmentary and structurally colored plumage patches. Using visual system-dependent methods, we showed that only some of the differences in plumage patches among the hybrid and its parent species would be perceivable by birds. Hyperspectral imaging is poised to become the gold standard for many animal coloration applications: comprehensive reflectance data—across the entire surface of an animal specimen—can be obtained in a matter of minutes. Our pipeline provides a practical and flexible roadmap for incorporating hyperspectral imaging into future studies of animal color.Animal coloration research has flourished recently but the uptake of hyperspectral imaging methods has been slow. This paper develops a user-friendly pipeline for hyperspectral imaging and highlights its advantages in measuring animal coloration by comparing two birds-of-paradise and their rare hybrid offspring.