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MORPHOMUSEUM: AN ONLINE PLATFORM FOR PUBLICATION AND STORAGE OF VIRTUAL SPECIMENS

Published online by Cambridge University Press:  27 April 2017

Renaud Lebrun  and
Maëva J. Orliac
Renaud Lebrun
Affiliation:
Laboratoire de Paléontologie, Institut des Sciences de l’Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier, place Eugène Bataillon, F-34095 Montpellier Cedex 05, France 〈renaud.lebrun@umontpellier.fr〉, 〈maeva.orliac@umontpellier.fr〉
Maëva J. Orliac
Affiliation:
Laboratoire de Paléontologie, Institut des Sciences de l’Évolution de Montpellier (ISE-M, UMR 5554, CNRS/UM/IRD/EPHE), c.c. 064, Université de Montpellier, place Eugène Bataillon, F-34095 Montpellier Cedex 05, France 〈renaud.lebrun@umontpellier.fr〉, 〈maeva.orliac@umontpellier.fr〉
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Abstract

Since the early 1990s, methods for the acquisition of three-dimensional (3-D) data and computer-assisted techniques for the visualization of such data have grown increasingly popular among biologists, paleontologists, and paleoanthropologists. However, thus far no standardized repository for complex virtual models based on 3-D digital data of specimens has emerged, whereas the need for researchers to provide access to 3-D models of specimens as well as the pressure imposed on authors by scientific journals to make original 3-D morphological data publicly available have increased. MorphoMuseuM (M3) aims to fill this gap. M3 is both a peer-reviewed scientific journal (M3 Journal) and a virtual specimen repository (M3 Repository). All scientific articles and their associated 3-D models deposited in M3 go through a formal review process. Each published model is given a DOI and a unique identifier code, which should be cited by researchers using this model in their scientific publications. In this paper, we describe the place of M3 among other online repositories for 3-D data, and explain how the growing community of biologists working with 3-D data can benefit from using M3.

Type
Research Article
Information
The Paleontological Society Papers , Volume 22: Virtual Paleontology , September 2016 , pp. 183 - 195
Copyright
Copyright © 2017, The Paleontological Society 

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References

Avila, L.S., Barré, S., Blue, R., Cole, D., Geveci, B., Hoffman, W.A., King, B., Law, C.C., Martin, K.M., Schroeder, W.J., and Squillacote, A.H., 2001, The VTK User’s Guide: Clifton Park, New York, Kitware, 536 p.Google Scholar
Baldock, R.A., and Burger, A., 2012, Biomedical atlases: Systematics, informatics and analysis: Advances in Experimental Medicine and Biology, v. 736, p. 655–677, DOI: 10.1007/978-1-4419-7210-1_39.CrossRefGoogle ScholarPubMed
Ballester-Ripoll, R., Suter, S.K., and Pajarola, R., 2015, Analysis of tensor approximation for compression-domain volume visualization: Computers & Graphics, v. 47, p. 34–47, DOI: 10.1016/j.cag.2014.10.002.Google Scholar
Blender Foundation, 2016, Blender: An open source 3-D creation suite: Amsterdam, The Netherlands, Stichting Blender Foundation, https://www.blender.org/ (accessed 20 February 2016).Google Scholar
Boistel, R., Herrel, A., Lebrun, R., Daghfous, G., Tafforeau, P., Losos, J. B., and Vanhooydonck, B., 2011, Shake rattle and roll: The bony labyrinth and aerial descent in squamates: Integrative and Comparative Biology, v. 51, p. 957–968, DOI: 10.1093/icb/icr034.Google Scholar
Boyer, D., Gunnell, G., Kaufman, S., and McGeary, T., 2017, MorphoSource—Archiving and sharing 3-D digital specimen data: The Paleontological Society Papers, v. 22, p. 157–181.Google Scholar
Cake Software Foundation, 2005, CakePHP: A web development framework running on PHP 7: Las Vegas, Nevada, Cake Software Foundation, http://cakephp.org/ (accessed 3 February 2016).Google Scholar
Conroy, G.C., and Vannier, M.W., 1984, Noninvasive three-dimensional computer imaging of matrix-filled fossil skulls by high-resolution computed tomography: Science, v. 226, p. 456–458, DOI: 10.1126/science.226.4673.456.Google Scholar
Cunningham, J.A., Rahman, I.A., Lautenschlager, S., Rayfield, E.J., and Donoghue, P.C.J., 2014, A virtual world of paleontology: Trends in Ecology & Evolution, v. 29, p. 347–357, DOI: 10.1016/j.tree.2014.04.004.Google Scholar
Faulwetter, S., Vasileiadou, A., Kouratoras, M., Dailianis, T., and Arvanitidis, C., 2013, Micro-computed tomography: Introducing new dimensions to taxonomy: ZooKeys, v. 263, p. 1–45, DOI: 10.3897/zookeys.263.4261.Google Scholar
Fourie, S., 1974, The cranial morphology of Thrinaxodon liorhinus Seeley: Annals of the South African Museum, v. 65, p. 337–400.Google Scholar
Gilissen, E., 2009a, Data sharing in the case of scanned museum collections: Suggestions for best practice: EDIT Newsletter, v. 14, p. 11–12.Google Scholar
Gilissen, E., 2009b, Museum collections, scanning, and data access: Journal of Anthropological Sciences, v., 89, p. 1–4.Google Scholar
Godinot, M., Crochet, J., Hartenberger, J., Lange-Badré, B., Russell, D., and Sigé, B., 1987, Nouvelles données sur les mammifères de Palette (Eocène inférieur, Provence). Münchner Geowissenschaftliche Abhandlungen A, v. 10, p. 273–288.Google Scholar
Lautenschlager, S., 2014, Palaeontology in the third dimension: A comprehensive guide for the integration of three-dimensional content in publications: Paläontologische Zeitschrift, v. 88, p. 111–121, DOI: 10.1007/s12542-013-0184-2.Google Scholar
Lautenschlager, S., and Rücklin, M., 2014, Beyond the print-virtual paleontology in science publishing, outreach and education: Journal of Paleontology, v. 88, p. 727–734, DOI: 10.1666/13-085.Google Scholar
Lebrun, R., 2014, ISE-MeshTools: A set of tools for editing, positioning, deforming, labeling, measuring, and rendering sets of 3-D meshes: Montpellier, France, Association Palaeovertebrata, http://morphomuseum.com/meshtools (accessed 3 February 2016).Google Scholar
Linnaeus, C., 1758, Systema Naturae per Regna tria Naturae, secundum Classes, Ordines, Genera, Species, cum Characteribus, Differentis, Synonymis, Locis, 10th ed.: Stockholm, Sweden, Laurentii, Slavi, 824 p.Google Scholar
Losano, F., Marinsek, G., Merlo, A.M., and Ricci, M., 1999, Computed tomography in the automotive field: Development of a new engine head case study, in DGZfP Proceedings, Computerized Tomography for Industrial Applications and Image Processing in Radiology, March 15–17 m 1999, Berlin, Germany: Berlin, Germany, Deutsche Gesellschaft für Zerstörungsfreie Prüfung e.V., BB67-CD, p. 65–73.Google Scholar
MeshLab, 2005, MeshLab: A processing system for 3D triangular meshes: La Jolla, California, Sourceforge Media, http://meshlab.sourceforge.net/ (accessed 20 February 2016).Google Scholar
Murienne, J., Ziegler, A., and Ruthensteiner, B., 2008, A 3D revolution in communicating science: Nature, v. 453, p. 450, DOI: 10.1038/453450d.Google Scholar
Peeters, F., Verbeeten, B. Jr., and Venema, H.W., 1979, Nobel Prize for medicine and physiology 1979 for A.M. Cormack and G.N. Hounsfield: Nederlands Tijdschrift Voor Geneeskunde, v. 123, p. 2192–2193.Google Scholar
Ponchio, F., 2009, Multiresolution structures for interactive visualization of very large 3D datasets [Ph.D. thesis]: Clausthal-Zellerfeld, Germany, Clausthal University of Technology, 107 p.Google Scholar
Potenziani, M., Callieri, M., Dellepiane, M., Corsini, M., Ponchio, F., and Scopigno, R., 2015, 3DHOP: 3D Heritage Online Presenter, p. 129–141, DOI: 10.1016/j.cag.2015.07.001.Google Scholar
Ramdarshan, A., Godinot, M., Bédécarrats, S., and Tabuce, R., 2015, Holotype specimen of Donrussellia magna, an adapiform primate from the early Eocene (MP7) of southern France: MorphoMuseuM, v. 1, no. 2, p. e2, DOI: 10.18563/m3.1.2.e2.Google Scholar
Rowe, T., and Frank, L.R., 2011, The disappearing third dimension: Science, v. 331, p. 712–714, DOI: 10.1126/science.1202828.Google Scholar
Shiraishi, N., Katayama, A., Nakashima, T., Shiraki, N., Yamada, S., Kose, K., and Takakuwa, T., 2015a, 3D models related to the publication: Morphology of the human embryonic brain and ventricles: MorphoMuseuM, v. 1, no. 3, p. e3, DOI: 10.18563/m3.1.3.e3.Google Scholar
Shiraishi, N., Katayama, A., Nakashima, T., Yamada, S., Uwabe, C., Kose, K., and Takakuwa, T, 2015b, Morphology and morphometry of the human embryonic brain: A three-dimensional analysis: NeuroImage, v. 115, p. 96–103, DOI: 10.1016/j.neuroimage.2015.04.044.CrossRefGoogle Scholar
Sketchfab, 2012, Sketchfab: A platform to publish and find 3-D and VR content: New York, Sketchfab, https://sketchfab.com/ (accessed 11 February 2016).Google Scholar
Spitzak, B., 1998–2015, FLTK: Fast Light Toolkit: A cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X: Seriss Corporation, http://www.fltk.org/index.php (accessed 3 February 2016).Google Scholar
Spoor, C.F., 1993, The comparative morphology and phylogeny of the human bony labyrinth [Ph.D. thesis]: Utrecht, The Netherlands, Utrecht University, 145 p.Google Scholar
Suter, S.K., Guitián, J.A.I., Marton, F., Agus, M., Elsener, A., Zollikofer, C.P.E., Gopi, M., Gobbetti, E., and Pajarola, R., 2011, Interactive multiscale tensor reconstruction for multiresolution volume visualization: IEEE Transactions on Visualization and Computer Graphics, v. 17, p. 2135–2143, DOI: 10.1109/TVCG.2011.214.Google Scholar
Suter, S.K., Makhynia, M., and Pajarola, R., 2013, TAMRESH—Tensor Approximation Multiresolution Hierarchy for interactive volume visualization: Computer Graphics Forum, v. 32, p. 151–160, DOI: 10.1111/cgf.12102.Google Scholar
Walter, T., Shattuck, D.W., Baldock, R., Bastin, M.E., Carpenter, A.E., Duce, S., Ellenberg, J., Fraser, A., Hamilton, N., Pieper, S., Ragan, M.A., Schneider, J.E., Tomancak, P., and Hériché, J.-K., 2010, Visualization of image data from cells to organisms: Nature Methods, v. 7, p. S26–S41, DOI: 10.1038/nmeth.1431.Google Scholar
Wind, J., 1984, Computerized X-ray tomography of fossil hominid skulls: American Journal of Physical Anthropology, v. 63, p. 265–282, DOI: 10.1002/ajpa.1330630303.Google Scholar
Zhexi, L., and Ketten, D.R., 1991, CT scanning and computerized reconstructions of the inner ear of multituberculate mammals: Journal of Vertebrate Paleontology, v. 11, p. 220–228.Google Scholar
Ziegler, A., Mietchen, D., Faber, C., von Hausen, W., Schöbel, C., Sellerer, M., and Ziegler, A., 2011, Effectively incorporating selected multimedia content into medical publications: BMC Medicine, v. 9, p. 17, DOI: 10.1186/1741-7015-9-17.Google Scholar
Ziegler, A., Ogurreck, M., Steinke, T., Beckmann, F., Prohaska, S., and Ziegler, A., 2010, Opportunities and challenges for digital morphology: Biology Direct, v. 5, p. 45, DOI: 10.1186/1745-6150-5-45.Google Scholar
Zonneveld, F.W., and Wind, J., 1985, High-resolution computed tomography of fossil hominid skulls: a new method and some results, in Tobias, P.V., ed., Hominid Evolution, Past, Present and Future: New York, Alan R. Liss, p. 427–736.Google Scholar
ZURB, 1998–2016, Foundation: A front-end framework for software design: Campbell, California, ZURB, http://foundation.zurb.com/ (accessed 20 February 2016).Google Scholar