Report Open Access

Rapid 3D capture methods in biological collections and related fields

Nieva de la Hidalga, Abraham; Rosin, Paul; Sun, Xianfang; van Walsun, Myriam; Wu, Zhengzhe

This report provides an overview of the status of 3D Digitisation in biological collections and related fields. The report is not intended to provide in depth analysis or description of the 3D digitisation methods as they have been documented in multiple documents
referred in the text. The report is designed to identify a) suitable 3D digitisation methods to achieve large scale digitisation and b) the issues which need to be addressed in order to increase 3D digitisation throughput using those methods. Accordingly, the report is
divided in six sections: 3D digitisation of NHC, 3D digitisation workflow, 3D Digitisation Methods, Areas of improvement, Ideal 3D digitisation workflow and conclusions. The first section establishes the need for 3D digitisation of Natural History Collections and
introduces the different types of 3D products which may be produced for as part of a digital specimen, with some examples. The second section defines a generic workflow for 3D digitisation consisting of tasks which are independent of the specific digitisation
methods applied. This section also defines the possible areas of improvement which can support increasing the throughput of digitisation workflows. The third section explores different digitisation methods which have applied to digitise NHC, defining which are the most suitable for mass imaging. The fourth section presents the existing solutions which could help improving the 3D digitisation workflows and practices looking at related fields, particularly cultural heritage. Section five brings together the digitisation methods and improvements to define the ideal 3D digitisation workflow and its prospects for being incorporated into the digitisation plans of natural history institutions in Europe. Finally, section six provides a summary of recommendations and a description of areas which may provide further improvements in 3D digitisation, such as fully integrated systems.

Files (10.6 MB)
Name Size
D3.7 ICEDIG_Rapid 3D capture methods in biological collections and related fields.pdf
10.6 MB Download
  • Anderson N. I. (2017) Item Driven Image Fidelity (IDIF) or "HITTING the Digital Capture Sweet Spot", Smithsonian Digitization.

  • Ariño, A. H., Galicia, D. (2005). Taxonomic Grade Images. In: Häuser et al. (eds.): Digital Imaging of Biological Type specimens. A Manual of Best Practice. Results from a study of the European Network for Biodiversity Information: 87-125. Stuttgart.

  • Cai, Z., Liu, X., Peng, X., Yin, Y., Li, A., Wu, J., & Gao, B. Z. (2016). Structured light field 3D imaging. Optics express, 24(18), 20324-20334.

  • Faulwetter, S., Vasileiadou, A., Kouratoras, M., Dailianis, T., & Arvanitidis, C. (2013). Micro-computed tomography: Introducing new dimensions to taxonomy. ZooKeys, (263), 1.

  • Fofi, David; T. Sliwa; Y. Voisin (January 2004). "A Comparative Survey on Invisible Structured Light" (PDF). SPIE Electronic Imaging — Machine Vision Applications in Industrial Inspection XII. San Jose, USA. pp. 90–97

  • Haston, E., et al. (2012) Developing integrated workflows for the digitisation of herbarium specimens using a modular and scalable approach. ZooKeys 209: 93–102 (2012)

  • Hereld, M., Ferrier, N. J., Agarwal, N., & Sierwald, P. (2017, October). Designing a high-throughput pipeline for digitizing pinned insects. In e-Science (e-Science), 2017 IEEE 13th International Conference on (pp. 542-550). IEEE.

  • Luhmann, T., Robson, S., Kyle, S. A., & Harley, I. A. (2006). Close range photogrammetry: principles, techniques and applications. Whittles.

  • Mathys, A., Brecko, J., Vandenspiegel, D., Cammaert, L., & Semal, P. (2016 September). Bringing collections to the digital era three examples of integrated high-resolution digitisation projects. In Digital Heritage, 2015 (Vol. 1, pp. 155-158). IEEE.

  • Nguyen, C. et. al. (2014). Capturing natural-colour 3D models of insects for species discovery and diagnostics. PloS one, 9(4), e94346

  • Salarelli, A. (2017). International Image Interoperability Framework (IIIF): a panoramic view. JLIS. it, 8(1), 50.

  • Van Zanten H. V., Van Spronsen E., Altenburg R. (2005) 3D Imaging for a Virtual Museum: Bird Type Specimens of the Zoological Museum Amsterdam. In: Häuser et al. (eds.): Digital Imaging of Biological Type specimens. A Manual of Best Practice. Results from a study of the European Network for Biodiversity Information: 265-275. Stuttgart.

  • Vollmar, A., Macklin, J.A., Ford, L. S. (2010) Specimen Digitization: Challenges and Concerns. Biodiversity Informatics, 7, 2010, pp. 93 – 112

  • Wilkinson, M. D., et. al. (2016). The FAIR Guiding Principles for scientific data management and stewardship. Scientific data, 3

  • Zhang, Y., Li, Z., Yang, W., Yu, P., Lin, H., & Yu, J. (2017, May). The light field 3D scanner. In Computational Photography (ICCP), 2017 IEEE International Conference on (pp. 1-9). IEEE.

All versions This version
Views 158158
Downloads 123123
Data volume 1.3 GB1.3 GB
Unique views 144144
Unique downloads 111111


Cite as