Ziegler A et al. (2010), Opportunities and challenges for digital morpho...

ECB-ART-41694

Biol Direct 2010 Jul 06;5:45. doi: 10.1186/1745-6150-5-45.

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Opportunities and challenges for digital morphology.

Ziegler A , Ogurreck M , Steinke T , Beckmann F , Prohaska S , Ziegler A .

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Advances in digital data acquisition, analysis, and storage have revolutionized the work in many biological disciplines such as genomics, molecular phylogenetics, and structural biology, but have not yet found satisfactory acceptance in morphology. Improvements in non-invasive imaging and three-dimensional visualization techniques, however, permit high-throughput analyses also of whole biological specimens, including museum material. These developments pave the way towards a digital era in morphology. Using sea urchins (Echinodermata: Echinoidea), we provide examples illustrating the power of these techniques. However, remote visualization, the creation of a specialized database, and the implementation of standardized, world-wide accepted data deposition practices prior to publication are essential to cope with the foreseeable exponential increase in digital morphological data.

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Genes referenced: cope LOC100887844 LOC105438433 LOC115925415

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	Figure 1. Virtual horizontal sections of 2D MRI scans of whole sea urchins (A, C) reveal distinct shapes of protractor muscles in Paracentrotus lividus (B) and Echinometra mathaei (D) (arrows). Magnetic resonance imaging was carried out in Berlin, Germany using a high-field MRI scanner with a 7 T super-conducting electromagnet (Bruker Biospin GmbH, Ettlingen, Germany). Image processing of the ~10 MB large raw image datasets was carried out using ImageJ 1.42q (NIH, Bethesda, USA) and its Volume Viewer plug-in on a standard office PC. The sea urchin (Echinodermata: Echinoidea) species shown here were collected in the wild (Paracentrotus lividus) or taken from a museum collection (Echinometra mathaei, NHM 1969.5.1.61-75).

	Figure 3. Various traditional and digital morphological visualization techniques, shown in an exemplary fashion using cidaroid sea urchins (Echinoidea: Cidaroida). A Habitus of a museum specimen of Eucidaris metularia (NHM 1969.5.1.15-40), aboral view. B Historical drawing of the internal anatomy of Cidaris cidaris, a closely related species - modified after Stewart [47]. C Volume rendering of the external anatomy of the specimen shown in A, based on a ~25 GB large Î¼CT dataset with 13.91 Î¼m isotropic resolution. D Virtual horizontal section of the Î¼CT dataset at the level of Aristotle's lantern (see also Fig. 2). E Surface rendering of the external and internal anatomy of the specimen shown in A based on a ~100 MB large 3D MRI dataset with 81 Î¼m isotropic resolution. F Virtual horizontal section of the MRI dataset at the level of Aristotle's lantern, digestive tract, and gonads. By clicking anywhere onto this figure, an interactive, partially labeled 3D model of the analyzed species will open (requires Adobe Acrobat Reader 8.0 or higher, see [10,43,44,46] for detailed information regarding 3D modeling and labeling). The museum specimen of Eucidaris metularia was photographed using a digital camera with 7.2 megapixel resolution (Exilim: Casio Computer Co., Tokyo, Japan). 3D visualization was carried out using volume rendering in VG Studio Max 2.0 (C) and threshold-based as well as manual segmentation followed by surface rendering in Amira 5.2 (E).

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