Interactive 3D volume rendering in biomedical publications

Abstract

We present three examples of interactive, 3D volume rendering models embedded in a PDF publication. The examples are drawn from three different morphological methods confocal microscopy, serial sectioning and microcomputed tomography performed on members of the phylum Mollusca. A description of the entire technical procedure from specimen preparation to embedding of the visual model including 3D labels in the document is provided. For comparison, volume rendering wit h standard visualisation software, and surface rendering incorporated in the 3D PDF figures, are provided. The principal advantages and disadvantages of the techniques and models are discussed. Volume rendering for serial sections is relatively workintensive, while confocal data have limitations in terms of 3D presentation. Volume renderings are normally downsampled in resolution to achieve a reasonable PDF file size, however intentional information is largely retained. We conclude that volume rendering of 3D data sets is a valuable technique and should become standard in PDF versions of biomedical publications. *Manuscript Click here to view linked References

Embedding and Publishing Interactive, 3-Dimensional, Scientific Figures in Portable Document Format (PDF) Files

“…To address this and improve upon our previous efforts (e.g. [9], [11]) we have included a command-line option in the xrw2pdf program that lets the user easily modify the opacity scaling ratios manually for the three slice sets until a satisfactory result—an equalized volume rendering—is obtained, prior to writing output PRC and PDF files. Figure 6 shows screen captures of the xrw2pdf program rendering nearby views but using different slice sets, without and with opacity rescaling.…”

“…Procedural notes: we have previously described our method for volume rendering in PDF [11] and published the corresponding S2PLOT program volren. For the volume rendering in Figure 5 we adapted and expanded this program into the new S2PLOT program xrw2pdf which provides a relatively simple but capable, end-user command-line program for generating interactive 3-d volume renderings of 3-d data as PDF figures.…”

“…Like others, our first successes [9]–[11] made use of (commercial) Adobe software (Adobe Acrobat 3D version 8) to read VRML97 scenes, in our case written by our own software library S2PLOT [12]. Other authors (e.g.…”

“…(Adobe Acrobat 3D has been superceded by Adobe Acrobat X Pro, and in-built support for adding 3-d figures was dropped — see File S1. A third-party plug-in from Tetra 4D is required to create 3-d PDF figures using the approach previously described ([9]–[11]). ) The created 3-d figures can then be embedded in existing PDF documents made by other applications.…”

Evolutionary phenomics and the emerging enlightenment of arthropod systematics

“…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).…”