Back to life: Techniques for developing high-quality 3D reconstructions of plants and animals from digitized specimens

Abstract

Expanded use of 3D imaging in organismal biology and paleontology has substantially enhanced the ability to visualize and analyze specimens. These techniques have improved our understanding of the anatomy of many taxa, and the integration of downstream computational tools applied to 3D datasets have broadened the range of analyses that can be performed (e.g., finite element analyses, geometric morphometrics, biomechanical modeling, physical modeling using 3D printing). However, morphological analyses inevitably present challenges, particularly in fossil taxa where taphonomic or preservational artifacts distort and reduce the fidelity of the original morphology through shearing, compression, and disarticulation, for example. Here, we present a compilation of techniques to build high-quality 3D digital models of extant and fossil taxa from 3D imaging data using freely available software for students and educators. Our case studies and associated step-by-step supplementary tutorials present instructions for working with reconstructions of plants and animals to directly address and resolve common issues with 3D imaging data. The strategies demonstrated here optimize scientific accuracy and computational efficiency and can be applied to a broad range of taxa.

Plant phenotyping relevance

植物を含む標本の3D画像データから高品質な形態モデルを構築する技術と手順が中心で、植物形態の取得・解析に再利用可能な方法論を提供している。

Code and data availability

The paper's Data Availability statement points to a public Figshare deposit containing the authors' 3D object files and tutorial materials used in the case studies (including plant specimen reconstructions), making it a paper-specific, publicly actionable asset.