Handbook of best practice and standards for 2D+ and 3D imaging of natural history collections

Abstract

Digitising a collection is key to make it last even after the physical objects are no longer available. Almost all of the techniques currently available to digitise a natural history collection in 2D+ and 3D are listed herein. The techniques are explained in a way that even one without any knowledge on the subject may understand their principle. The strong and weak points of the techniques are discussed, and an overview of suitable collections and specimens are given for each one of them. Also, plenty of examples already digitised with each technique are provided together with the links to visualise them in 3D. After explaining all the different digitisation options, the subsequent chapters provide information on how to improve the 2D+ and 3D digital twins of the specimens and techniques are compared to each other by means of test specimens. These give a fast overview of the capabilities of the digitisation techniques. Possible solutions to avoid digitisation errors are equally provided. Lastly, the dissemination of the results and the data management of the 3D models are briefly discussed in the final chapters. Also, a large chapter is provided with several workflows that can be followed to get the best possible results.

A new giant sauropod,Australotitan cooperensisgen. et sp. nov., from the mid-Cretaceous of Australia

“…Tradeoffs also include ease of access to capture the specimens in the first instance, which includes lighting, physical location, speed of capture and ultimately resolution and fidelity of the final digital 3-D geometry. This has led to the development of some standards and procedures of capture that may assist collection managers, curators and researchers when deciding about the relative advantages and disadvantages of different scanning procedures and taking into account these tradeoffs ( Bitelli et al, 2020 ; Brecko & Mathys, 2020 ; Lautenschlager, 2016 ; Le Cabec & Toussaint, 2017 ; Otero et al, 2020 ; Vidal & Díez Díaz, 2017 ). However, it is unlikely that all standards can be met at all times, and in our present experience, this was the case.…”

scAnt—an open-source platform for the creation of 3D models of arthropods (and other small objects)

“…High-quality 3D models of arthropods may aid in both conservation and outreach, as they bring with them the following advantages (Nguyen et al, 2014;Galantucci, Pesce & Lavecchia, 2015;Erolin, Jarron & Csetenyi, 2017;Ströbel et al, 2018;Cobb et al, 2019;Brecko & Mathys, 2020):…”

“…This issue is particularly severe for rare and valuable specimens such as holotypes, which can be difficult to access despite their scientific importance. In recognition of these limitations, significant efforts have been underway to digitise natural history collections (Beaman & Cellinese, 2012;Blagoderov et al, 2012;Mantle, La Salle & Fisher, 2012;Nguyen et al, 2017Nguyen et al, , 2014Hudson et al, 2015;Martins et al, 2015;Galantucci, Pesce & Lavecchia, 2016;Erolin, Jarron & Csetenyi, 2017;Ströbel et al, 2018;Galantucci, Guerra & Lavecchia, 2018;Qian et al, 2019;Brecko & Mathys, 2020). Such a cybertaxonomy has been predicted to revolutionise collaborative taxonomy, and fundamentally change formal and public taxonomic education (Zhang, Gao & Caelli, 2010;Wheeler et al, 2012).…”

“…Photographs are doubtlessly useful, but by definition contain substantially less information than the original specimen, as they are restricted to a single image plane (Nguyen et al, 2014;Ströbel et al, 2018). Even obtaining simple 1D measurements from 2D images is error-prone, due to parallax errors and intra-observer variability, which is larger for measurements obtained from 2D photographs compared to 3D models (Ströbel et al, 2018;Qian et al, 2019;Brecko & Mathys, 2020). As a consequence, the "gold standard" for digitisation are photorealistic and anatomically accurate 3D models (Wheeler et al, 2012).…”

“…Perhaps the most promising method for the creation of 3D models is photogrammetric reconstruction, which retains colour information, and represents an excellent compromise between portability, price and quality (Mathys, Brecko & Semal, 2013;Brecko & Mathys, 2020). To the best of our knowledge, there exist two photogrammetry devices specifically designed for the creation of 3D models of arthropods (Nguyen et al, 2014;Ströbel et al, 2018).…”