Figure 1.
Flow diagram for creating 3-d PDF figures with S2PLOT.
The final output is a PDF file generated with LaTeX, including one or more 3-d figures, embedded with movie15.sty, created via PRC export from the user's S2PLOT program.
Figure 2.
The standard S2PLOT 3-d PDF space (3-d figure).
This simple figure, a wireframe cube with faces labelled, provides a simple example for becoming familiar with the standard 3-d PDF toolbar, and the default S2PLOT extensions (keyboard controls) implemented via JavaScript. When reading File S2, with a PDF reader that supports 3-d figures (i.e. Adobe Reader and Adobe Acrobat, for PC or Mac) the 3-d mode will be activated automatically. Otherwise a regular, static 2-d figure will be displayed.
Table 1.
Standard S2PLOT 3-d PDF keyboard controls.
Figure 3.
RNA polymerase alpha subunit (alpha CTD) of the Escherichia coli organism (3-d figure).
An S2PLOT program to construct 3-d visualisations of molecules from the Protein Data Bank was used to render this part of the E. coli organism. Atoms are coloured according to hydropathy. When reading File S2, atoms and bonds can be toggled in and out of the visualisation by expanding the model tree, or by using hyperlinks. This figure also demonstrates the optional feature of a “poster image” which must be clicked (in File S2) to activate the 3-d figure. Data downloaded from the Protein Data Bank; original source [15].
Figure 4.
RNA polymerase alpha subunit (alpha CTD) of the Escherichia coli organism.
(a) Excerpt of the PDB text-format description file for this protein; and (b) Jmol 3-d projection obtained at the Research Collaboratory for Structural Bioinformatics (http://home.rcsb.org) PDB site.
Figure 5.
Volume rendering of a magnetic resonance angiography (MRA) image (3-d figure).
The xrw2pdf utility was used to balance the opacity of each slice set to minimise difference at the (diagonal) transitions between slice sets. Data downloaded from the OsiriX Foundation and the University Hospital of Geneva; original identifier CETAUTOMATIX (Normal cardiac MRI and MRA study. Mild aortic and tricuspid valves regurgitation.) When reading File S2, click to activate the 3-d figure (when using Adobe Acrobat or Adobe Reader).
Figure 6.
Demonstration of equalized volume rendering using opacity rescaling in xrw2pdf.
(a) volume rendering of ZY slices; and volume rendering of XZ slices from a nearby viewpoint (b) without and (c) with opacity rescaling. Opacity rescaling dramatically improves the transition between renderings of different, oblique slice sets.
Figure 7.
Magnetic resonance angiography slices.
A subset of the 2-d image slices exported from OsiriX prior to stacking into the 3-d image used to generate Figure 5.
Figure 8.
Validation of volume rendering in 3-d PDF.
Top row: screen captures of the full-resolution MRA image, volume rendered in (a) S2PLOT, (b) 3-d PDF, and (c) OsiriX. Bottom row: smoothed, greyscale difference images between (d) the S2PLOT and 3-d PDF visualisations, and (e) the OsiriX and 3-d PDF visualisations. See text for further details and discussion.
Figure 9.
Surface rendering of the outer cerebral cortex (pial surface), and optional overlay of correlated functional activations corresponding to selected, recognised rest state networks (accessed via the “Views” menu when reading File S2).
Functional MRI data set courtesy Govinda Poudel; cortical surface extraction by FreeSurfer (http://surfer.nmr.mgh.harvard.edu/).
Figure 10.
(a) FreeSurfer tkmedit rendering of T1-weighted structural MR image and cross-section through extracted pial surface; and (b) FreeSurfer tksurfer 3-d rendering of the pial surface.
Figure 11.
Volume rendering, and surface segmentation of the digestive tract, of a juvenile specimen of the marine pulmonate snail Ovatella myosotis (3-d figure).
When reading File S2 the 3-d figure is automatically activated. Sample (total length: 0.86 mm) prepared as described in [23]; stacked, optical microscopy images processed and manually segmented as per [18].
Figure 12.
Laughing Kookaburra (Dacelo novaeguineae) skull and jaw anatomy (3-d figure).
Manually segmented meshes simplified in MeshLab. When reading File S2, click to activate the 3-d figure (when using Adobe Acrobat or Adobe Reader).
Figure 13.
Validation of surface rendering in 3-d PDF (1).
Left column: screen captures of the Laughing Kookaburra skull and jaw anatomy surface-rendered in (a) S2PLOT, (b) 3-d PDF and (c) Rhinoceros. Right column: corresponding edge-detected images. See text for further details and discussion.
Figure 14.
Validation of surface rendering in 3-d PDF (2).
Edge-detected images from screen captures of the Laughing Kookaburra skull and jaw anatomy surface-rendered in: (a) S2PLOT (blue) and 3-d PDF (orange); (b) 3-d PDF (orange); and (c) Rhinoceros (blue) and 3-d PDF (orange). See text for further details and discussion.