Embedding 3D models of biological specimens in PDF publications

Abstract

By providing two examples, the option for embedding 3D models in electronic versions of life science publications is presented. These examples, presumably representing the first such models published, are developmental stages of an evertebrate (Patella caerulea, Mollusca) and a vertebrate species (Psetta maxima, Teleostei) obtained from histological section series reconstruction processed with the software package Amira. These surface rendering models are particularly suitable for a PDF file because they can easily be transformed to a file format required and components may be conveniently combined and hierarchically arranged. All methodological steps starting from specimen preparation until embedding of resulting models in PDF files with emphasis on conversion of Amira data to the appropriate 3D file format are explained. Usability of 3D models in PDF documents is exemplified and advantages over 2D illustrations are discussed, including better explanation capabilities for spatial arrangements, higher information contents, and limiting options for disguising results by authors. Possibilities for additional applications reaching far beyond the examples presented are suggested. Problems such as long-term compatibility of file format and hardware plus software, editing and embedding of files, file size and differences in information contents between printed and electronic version will likely be overcome by technical development and increasing tendency toward electronic at the cost of printed publications. Since 3D visualization plays an increasing role in manifold disciplines of science and appropriate tools for the popular PDF format are readily available, we propose routine application of this way of illustration in electronic life science papers. Microsc. Res. Tech. 71:778-786, 2008. V

Interactive 3D volume rendering in biomedical publications

“…The present example, the metamorphic competent larva of the limpet Patell a caerulea (Linné, 1758), is the same specimen as has been given in Ruthensteiner & Heß (2008). The results in VR (Figs 2A,B,D,G,H) are similar to the final stack images (Fig.…”

“…Typically, substructures are discerned by a manual segmentation procedure followed by surface generation for each component using a standard software algorithm (for general procedures see e.g. Ruthensteiner, 2008;Ruthensteiner & Heß, 2008) .…”

“…The advantage in using our approach lies in the capacity to produce an interactive volume rendering that is highly-representative of the final result that will be rendered in the 3D PDF figure were subsequently exported to a PDF file. See also Ruthensteiner & Heß (2008) and Kumar et al (2008) for the procedure of PDF embedding of models . PDF settings were prepared with ADOBE ACROBAT.…”

Evolutionary phenomics and the emerging enlightenment of arthropod systematics

“…The Portable Document Format (PDF) can now integrate SR three-dimensional models (supplementary file available at http://dx.doi.org/10.6084/m9.figshare.94272) as embedded, interactive figures (Ruthensteiner and Heß 2008), which makes distribution of these illustrations a relatively trivial exercise; only common, free software (namely Adobe Acrobat Reader) is required. Volume rendered models currently can only be published as supplementary files, but the ability to incorporate them into PDFs will likely happen in the near future (Ruthensteiner et al 2010).…”

Portable Document Format File Containing the Surface Models to Learn the Stereoscopic Shape of Foot Muscles

“…The purpose of this work is to distribute more profitable models, contained in a portable document format file. Unlike other products, the PDF file, which is downloadable free of charge, can also be manipulated off-line to display the wanted surface models in real time (Ruthensteiner & Hess, 2008;Kumar et al, 2010;Phelps et al, 2012;Shin et al, 2012aShin et al, , 2012bPark et al, 2013;Kim et al, 2014).…”