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. 2019 Feb;280(2):223-231.
doi: 10.1002/jmor.20938.

A Comprehensive and User-Friendly Framework for 3D-data Visualisation in Invertebrates and Other Organisms

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Free PMC article

A Comprehensive and User-Friendly Framework for 3D-data Visualisation in Invertebrates and Other Organisms

Thomas L Semple et al. J Morphol. .
Free PMC article

Abstract

Methods for 3D-imaging of biological samples are experiencing unprecedented development, with tools such as X-ray micro-computed tomography (μCT) becoming more accessible to biologists. These techniques are inherently suited to small subjects and can simultaneously image both external and internal morphology, thus offering considerable benefits for invertebrate research. However, methods for visualising 3D-data are trailing behind the development of tools for generating such data. Our aim in this article is to make the processing, visualisation and presentation of 3D-data easier, thereby encouraging more researchers to utilise 3D-imaging. Here, we present a comprehensive workflow for manipulating and visualising 3D-data, including basic and advanced options for producing images, videos and interactive 3D-PDFs, from both volume and surface-mesh renderings. We discuss the importance of visualisation for quantitative analysis of invertebrate morphology from 3D-data, and provide example figures illustrating the different options for generating 3D-figures for publication. As more biology journals adopt 3D-PDFs as a standard option, research on microscopic invertebrates and other organisms can be presented in high-resolution 3D-figures, enhancing the way we communicate science.

Keywords: Blender; Drishti; Meshlab; PDF; computed tomography.

Figures

Figure 1
Figure 1
Framework for 3D‐data manipulation and visualisation, including four workflows (two basic and two advanced) for creating PDF figures from 3D‐data using the programs Drishti, MeshLab and Blender. The four images provide examples of the figures achievable from each of the corresponding workflows. Software used at each step is highlighted in bold, and file formats in italics
Figure 2
Figure 2
3D‐volume rendering of a female thynnine wasp head (Hymenoptera: Thynninae: Ariphron sp.) produced using the Basic Drishti workflow. This image exemplifies the detail available in μCT scan data, with fine setae and antennal sensory pores clearly visible
Figure 3
Figure 3
Note: This video can be viewed in the Supporting Information online . (a) 3D‐rendering of the terminal abdominal segments of a male thynnine wasp (Hymenoptera: Thynninae: Catocheilus sp.). (b) Virtual dissection and segmentation of the male genitalia (red), generated using the Advanced Drishti workflow. Scale bar = 1 mm
Figure 4
Figure 4
Note: To enable the interactive function of this figure, open the PDF in Adobe Reader program or web plug‐in. Interactive 3D‐PDF of a female thynnine wasp head (Thynninae: Ariphron sp.) generated using the basic MeshLab workflow. This 3D‐mesh has been annotated to provide a self‐contained resource for science communication and education. A key benefit of presenting such data from primary research in the PDF format, is that those images can subsequently be used in education or for science communication without specialised software
Figure 5
Figure 5
Note: To enable the interactive function of this figure, open the PDF in Adobe Reader program or web plug‐in. Interactive 3D‐PDF of a female thynnine wasp head (Thynninae: Ariphron sp.) generated using the advanced blender workflow. This 3D‐mesh has been segmented and labeled to provide a highly informative scientific figure. Here, we also provide a basic example of how ‘rigging’ can be used to virtually reposition limbs or other components (in this case the mandibles of the wasp head). This can be thought of as ‘virtual insect pinning’, providing a standardized layout to facilitate examination, with the same reasoning as traditional insect pinning

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