Interactive 3D volume rendering in biomedical publications.

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 with standard visualization 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 work-intensive, 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.

[1]  A. Wanninger,et al.  Comparative larval myogenesis and adult myoanatomy of the rhynchonelliform (articulate) brachiopods Argyrotheca cordata, A. cistellula, and Terebratalia transversa , 2009, Frontiers in Zoology.

[2]  Hirokazu Hasegawa.  Laser Scanning Confocal Microscopy , 2006 .

[3]  A. Webb,et al.  Introduction to biomedical imaging , 2002 .

[4]  O Majdani,et al.  Evaluation of surface and volume rendering in 3D-CT of facial fractures. , 2006, Dento maxillo facial radiology.

[5]  Jonathan K Tyzack.  Dragging (and zooming and rotating) publication of 3D molecular structures into the 21st century. , 2008, Trends in biochemical sciences.

[6]  Bernhard Ruthensteiner,et al.  Soft Part 3D visualization by serial sectioning and computer reconstruction , 2008 .

[7]  Jayaram K. Udupa,et al.  Surface and volume rendering in three-dimensional imaging: A comparison , 1991, Journal of Digital Imaging.

[8]  E. Ritman.  Micro-computed tomography-current status and developments. , 2004, Annual review of biomedical engineering.

[9]  Christopher J. Fluke,et al.  An Advanced, Three-Dimensional Plotting Library for Astronomy , 2006, Publications of the Astronomical Society of Australia.

[10]  Alexander Gruhl.  Serotonergic and FMRFamidergic nervous systems in gymnolaemate bryozoan larvae , 2009, Zoomorphology.

[11]  S. Richter,et al.  Morphology of the haemolymph vascular system in Tanaidacea and Cumacea: - implications for the relationships of "core group" Peracarida (Malacostraca; Crustacea). , 2008, Arthropod structure & development.

[12]  B. Metscher.  MicroCT for comparative morphology: simple staining methods allow high-contrast 3D imaging of diverse non-mineralized animal tissues , 2009, BMC Physiology.

[13]  E. Fishman,et al.  Three-dimensional volume rendering of spiral CT data: theory and method. , 1999, Radiographics : a review publication of the Radiological Society of North America, Inc.

[14]  Klaus Mueller,et al.  Overview of Volume Rendering , 2005, The Visualization Handbook.

[15]  B. Runnegar,et al.  Aesthete canal morphology in twelve species of chiton (Polyplacophora) , 2007 .

[16]  A. Sakellariou,et al.  Imaging honey bee brain anatomy with micro-X-ray-computed tomography , 2008, Journal of Neuroscience Methods.

[17]  Matthias Epple,et al.  X-ray microcomputer tomography for the study of biomineralized endo- and exoskeletons of animals. , 2008, Chemical reviews.

[18]  David H. Laidlaw,et al.  The Visualization Handbook. Painting and Visualization , 2005 .

[19]  C. Faber,et al.  Systematic comparison and reconstruction of sea urchin (Echinoidea) internal anatomy: a novel approach using magnetic resonance imaging , 2008, BMC Biology.

[20]  Elena P. Ivanova,et al.  Effect of ultrafine-grained titanium surfaces on adhesion of bacteria , 2009, Applied Microbiology and Biotechnology.

[21]  Rachel J. Arnold,et al.  A New Genus and Species of the Shallow-Water Anglerfish Family Tetrabrachiidae (Teleostei: Lophiiformes: Antennarioidei) from Australia and Indonesia , 2009, Copeia.

[22]  David G. Heath,et al.  Skeletal 3-D CT: advantages of volume rendering over surface rendering , 1996, Skeletal Radiology.

[23]  Stuart R. Stock,et al.  MicroComputed Tomography: Methodology and Applications , 2008 .

[24]  J. Conchello,et al.  Three-dimensional imaging by deconvolution microscopy. , 1999, Methods.

[25]  S. Maslakova,et al.  Larval Development With Transitory Epidermis in Paranemertes peregrina and Other Hoplonemerteans , 2009, The Biological Bulletin.

[26]  Bernhard Ruthensteiner,et al.  3D interactive microanatomy of Omalogyra atomus (Philippi, 1841) (Gastropoda, , 2008 .

[27]  Scott E. Fraser,et al.  Digital Three-Dimensional Atlas of Quail Development Using High-Resolution MRI , 2007, TheScientificWorldJournal.

[28]  R. Loesel,et al.  Three-dimensional reconstruction of mushroom body neuropils in the polychaete species Nereis diversicolor and Harmothoe areolata (Phyllodocida, Annelida) , 2009, Zoomorphology.

[29]  A. Wanninger,et al.  Neurogenesis of cephalic sensory organs of Aplysia californica , 2007, Cell and Tissue Research.

[30]  An introduction to confocal imaging. , 1999, Methods in molecular biology.

[31]  R. Croll,et al.  Major muscle systems in the larval caenogastropod, Ilyanassa obsoleta, display different patterns of development , 2009, Journal of morphology.

[32]  Henry Fuchs,et al.  Optimal surface reconstruction from planar contours , 1977, CACM.

[33]  E. Fishman,et al.  Volume rendering versus maximum intensity projection in CT angiography: what works best, when, and why. , 2006, Radiographics : a review publication of the Radiological Society of North America, Inc.

[34]  Michael W. Davidson,et al.  LASER SCANNING CONFOCAL MICROSCOPY , 2005 .

[35]  Maria Byrne,et al.  Three‐dimensional reconstruction of the odontophoral cartilages of Caenogastropoda (Mollusca: Gastropoda) using micro‐CT: Morphology and phylogenetic significance , 2009, Journal of morphology.

[36]  Christopher J. Fluke,et al.  Incorporating interactive three-dimensional graphics in astronomy research papers , 2007, 0709.2734.

[37]  Pat Hanrahan,et al.  Volume Rendering , 2020, Definitions.

[38]  Andreas Ziegler,et al.  Grasping molecular structures through publication-integrated 3D models. , 2008, Trends in biochemical sciences.

[39]  B. Ruthensteiner,et al.  Embedding 3D models of biological specimens in PDF publications , 2008, Microscopy research and technique.