Computed 3D visualisation of an extinct cephalopod using computer tomographs.

The first 3D visualisation of a heteromorph cephalopod species from the Southern Alps (Dolomites, northern Italy) is presented. Computed tomography, palaeontological data and 3D reconstructions were included in the production of a movie, which shows a life reconstruction of the extinct organism. This detailed reconstruction is according to the current knowledge of the shape and mode of life as well as habitat of this animal. The results are based on the most complete shell known thus far of the genus Dissimilites. Object-based combined analyses from computed tomography and various computed 3D facility programmes help to understand morphological details as well as their ontogentical changes in fossil material. In this study, an additional goal was to show changes in locomotion during different ontogenetic phases of such fossil, marine shell-bearing animals (ammonoids). Hence, the presented models and tools can serve as starting points for discussions on morphology and locomotion of extinct cephalopods in general, and of the genus Dissimilites in particular. The heteromorph ammonoid genus Dissimilites is interpreted here as an active swimmer of the Tethyan Ocean. This study portrays non-destructive methods of 3D visualisation applied on palaeontological material, starting with computed tomography resulting in animated, high-quality video clips. The here presented 3D geometrical models and animation, which are based on palaeontological material, demonstrate the wide range of applications, analytical techniques and also outline possible limitations of 3D models in earth sciences and palaeontology. The realistic 3D models and motion pictures can easily be shared amongst palaeontologists. Data, images and short clips can be discussed online and, if necessary, adapted in morphological details and motion-style to better represent the cephalopod animal.

Introduction

The creation of 3D models of fossils (e.g. cephalopods) helps visualising interpretation and may serve for mechanical models. 3D models of fossil specimens have become increasingly popular, providing more or less accurate reconstructions of volumes, spatial distribution, orientation and size of fossils in a sample as well as of biostratinomic and diagenetic processes. Numerous complementary techniques have been advanced in recent years. These provide 3D datasets of palaeontological objects and involve both surface and volume scanning methods (e.g. microtomography). Laser scanning (airborne, terrestrial or desktop scanners) of surface morphology, point cloud data generated from digital images, or computed tomography down to a few microns (or even smaller) of spatial resolution are increasingly employed for geoscientific investigations, using an equally variable range of processing techniques and software packages. Numerous papers (e.g. Marschallinger, 2001; Maloof et al., 2010; Mayrhofer and Lukeneder, 2010; Kruta et al., 2011; Marschallinger et al., 2011; Lukeneder and Lukeneder, 2011; Saupe et al., 2012) show the multitude of applications of 3D geometrical models in palaeontological studies. The great variability, the wide range of applications and the analytical techniques in the fossil record are demonstrated for dinosaurs (Rayfield et al., 2001, 2007; Balanoff et al., 2008; Witmer and Ridgely, 2009; Fortuny et al., 2011; Tsuihiji et al., 2011; Knoll et al., 2012), lizards (Polcyn et al., 2002), birds (Rowe et al., 2001; Degrange et al., 2010; Zelenitsky et al., 2011), fishes (Gai et al., 2011), mammals (Luo et al., 2002), molluscs (Hoffmann and Zachow, 2011), brachiopods (Gaspard et al., 2011), plants (Friis et al., 2007; Scott et al., 2009), algal or acritarch fossils (Cunningham et al., 2012), and protists (Donoghue et al., 2006; Dong et al., 2010; Huldtgren et al., 2011). The latter papers also outline possible limitations of 3D models in earth sciences and in palaeontology.

The main goal of this paper is to present methods and possibilities for visualisation of palaeontological material based on computed tomography and palaeontological features (e.g., morphology; Fig. 1). Using computer facilities such as Nurbs Realtime Editor, CAD Application Rhinoceros® 4.0, Model Editor, 3d Studio Max® from Autodesk® or 3D Coat© yield a more detailed picture of the morphology of the genus Dissimilites and its swimming habits. The result is the computed 3D model of the fossil cephalopod Dissimilites itself along with the reconstruction of a 3D model in the framework of motion pictures showing animated animals in their habitat. A 3-year project of the Austrian Science Fund (FWF P20018-N10) resulted in accurate reconstructions of cephalopods and demonstrated the increasing importance of 3D models in palaeontology.

Fig. 1

Principal steps in 3D visualisation of palaeontological material such as fossil cephalopods.

Morphological details obtained by computed tomography

Noninvasive techniques allow to process great volumes of information, detected by computer tomography on fossils material, without causing any alteration. The tomography scans were made at the Upper Austria University of Applied Science in Wels. The 3D computed tomography (CT) device RayScan 250 E is a 3D CT system with two X-ray sources (a 225 kV micro-focus and a 450 kV mini-focus X-ray tube) for the inspection of a wide variety of parts, ranging from micro-objects (high resolution) to macroscopic ones (large penetration length). The system is additionally equipped with a 2048×2048 pixels flat-panel detector; it absorbs energy of the X-rays and reemits the absorbed energy in the form of light, which can be detected. In the case of an industrial CT-system, the specimen is rotated by 360° and at each pre-defined angle step a 2D-projection image is captured. The complete set of projection images is then reconstructed to 3D volume data using a mathematical algorithm. The data consists of volumetric pixels (voxels), whose size limits the detail detectability. For each fossil part, the optimal voxel size and tube voltage were set according to the specimen's dimensions. A more detailed introduction to computed tomography is beyond the scope of this article. For the details of X-ray computed tomography as a technique of imaging and quantification of internal features of sediments and fossils see Mees et al. (2003). The non-destructive CT provides the basal information on morphological features of the respective fossil cephalopod.

Palaeontological material

The shape data derived from a recently described species, namely Dissimilites nov. sp. (Lukeneder and Lukeneder, in press; Fig. 2). This fossil cephalopod originates from the Puez locality (Dolomites, northern Italy). The material was collected within the FWF project P20018-N10 and is stored at the Natural History Museum in Vienna (NHMW, holotype 2012/0002/0001). The heteromorph ammonoid was collected by Susanne Lukeneder from Lower Barremian beds (approx. 127 million years old) at the Puez section.

Fig. 2

(a) Dissimilites specimen coated with ammonium chloride (600 dpi). Asterisk marks the beginning of body chamber, (b) computed tomography slices from the specimen (due to the limonitic preservation in white) and the embedding limestone (grey). Performed on a RayScan 250 E, with a 450 kV mini-focus X-ray tube and a 2048×2048 pixel flat panel detector (cone beam reconstruction), (b1–b5) frontal slices and (b6–b7) axial sclices. Slice spacing is 0.11 mm/pixel space, (c) image of Dissimilites uncoated with limonitic preservation (yellow to orange, 600 dpi). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

The outcrop is situated on the Puez-Odle-Gardenaccia Plateau in the Dolomites (maps Trentino—Alto Adige; South Tyrol; Lukeneder, 2010). The exact position is about 30 km northeast of Bozen (E 011°49′15″, N 46°35′30″; Lukeneder, 2010,2012, 2012). A detailed description of the geology and lithostratigraphy is given in Lukeneder (2010).

Visualisation and motion pictures

Macrophotography

Detailed images of the specimen were taken with a Kodak Professional DCS Pro combined with the photo device Stereo Discovery V20 with AxioCam MR5 Zeiss. All images have the same file structure with Dissimilites.tiff, 600 dpi resolution. Black-and-white images are combined with full colour images for high visibility of fossil edges and details (Fig. 2).

Computed tomography

3D computed tomography was performed at a 225 kV microfocus and a 450 kV mini-focus X-ray tube. The specimen and the embedding fossiliferous marly limestone were tomographed frontally and axially (angle of 90°; Figs. 2 and 3). Frontal and axial slice-images were animated to videos as frontal.avi and axial.avi motion pictures. 654 frontal slices (000.jpg-654.jpg; 342 MB) with 0.11 mm/pixel space and 1 619 axial slices (0000.jpg-1619.jpg, 376 MB) with 0.11 mm/pixel space were produced. Measurements were performed with durations of 56, 68 and 92 min. Voxel sizes were 95 and 75.01 μm. Electrical voltage was at 220 and 400 kV with 425 and 1500 μA. Exposure time was at 600, 999, and 2000 ms. 1440 projections with a Cu pre-filter 1.0, 2.0 and 4.0 mm were made. Additionally, the surface (e.g., stone vs. air) was rendered to image the cephalopod's morphology (Fig. 3f).

Fig. 3

(a–e) Normal Map and visualisation onto a surface inside a 3D Realtime Editor. Virtual light source was tilted in different directions to gain plasticity from highlights and shadows, (f) rendered surface model based on data from a RayScan 250 E, with a 450 kV mini-focus X-ray tube. Spacing of rendered slices is 0.11 mm/pixel space (600 dpi).

3D visualisation and motion pictures of fossil cephalopods

The modelling procedure of the fossil cephalopod is based on line drawings on which successive cross-sections were fitted. Additionally, the series of CT images turned out to be an essential source to understand the fossil's morphology and shape. Both were used to draw the cross-sections used in the later-processed 3D model. The images present a grey scale spectrum which was further refined by converting its height information, ranging from darker to lighter areas, to a so-called “Normal Map” image. This helped to refine the visual appearance and understand various delicate structures. The process involved projecting this Normal Map onto a surface inside a 3D Realtime Editor and then introducing a virtual light source, which was tilted in different directions to gain plasticity from highlights and shadows (Fig. 3).

The 3D modelling procedure was carried out in different stages using different 3D modelling and animation software facilities and programmes (e.g., Nurbs Realtime Editor, Model Editor or 3d Studio Max® from Autodesk®), each specialized for its defined task. The first step was to achieve a precise volume model of the fossil cephalopod, followed by refining its geometric shape by adjusting scale and patterns to place the discrete spines. The final texture was created by colouration and image information directly on its surface in preparation for the final rendering and animation process (Fig. 4).

Fig. 4

(a) Visualisation by final rendering in Nurbs Model Editor and 3d Studio Max© by Michael Klein (7reasons), (b–c) vectorisation and geometrical refinement in 3D Studio Max, (d) imported geometries with paint application tools, (e) scene setup for the final rendering in 3D Studio Max, (f) modelling process in the Kinematic Bone System.

The outline of Dissimiltes intermedius was vectorised and imported into a CAD Application (Rhinoceros® 4.0), which is orientated to create 3D geometry from so-called NURBS (Non Unified Rational B-Splines), and hereafter used as a guideline to extrude the prepared cross-sections along its edges. Various other techniques had been tested before, including the manual extrusion of the sections or their replication, but with unsatisfactory results.

To refine surface features, the NURBS Model was brought into 3D Studio Max® from Autodesk®. The detailed morphology features visible on the macrophotographs and CT images of the source material were used to determine the size and location of ribs and spines. These were then modelled and placed by hand. The soft tissue of the cephalopod animal was processed by 3D Studio Max®, starting with a basic shape, which was subsequently refined by precision of morphological characters (Fig. 4). It has to be noted that not much is known on soft parts of ammonites (Lehmann, 1990; Maeda and Seilacher, 1996), their habitats (Jacobs et al., 1994a,b; Westermann, 1996; Lukeneder et al., 2010), and the locomotion of fossil cephalopods (Jacobs, 1992, 2001; Jacobs and Chamberlain, 1996; Monks and Young, 1998; Klug and Korn, 2004).

The resulting geometries were exported to an additional programme specialized in 3D texturing and painting (3D Coat©). UVW mapping allows direct painting on the 3D surface of the generated models. UVW describes the coordinates of the underlying mesh in its x-, y-, and z-axis and translates a given texture or coloration to distinct areas or morphological features. For the actual process of painting, various maps were gathered from existing images and placed in the background of the application; the 3D model was placed in front, and parts of these images were projected onto a special marked area.

The final geometries were then re-imported to 3D Studio Max© for the animation and rendering setup (Fig. 4). For the animation of the animal's body, virtual “elements” were created by the inverse kinematic bones system and linked to a hierarchy with inverse kinematic constraints (Fig. 4f). This allows the animator to move several bones by using only the last link of this hierarchy. The surrounding scenery was assembled with a simple plane for the sea floor, a parametric geometry serving as a water plane, and the setting of virtual lights and ambient influences (e.g., lights through waves; Fig. 5; Animation 1).

Fig. 5

(a–h) 3D reconstruction of successive ontogenetic stages in the fossil cephalopod Dissimilites (600 dpi). (a) Cyrtocone juvenile animal. (b–d) Mid-aged animal with straight shell stages. (e–h) Different views of the adult, mature animal.

Animation 1

Representative frame still (timeslice at sec. 18) from the attached 3D animation (Dissimilites.mp4; 11.1 MB) of the Cretaceous cephalopod Dissimilites in different ontogentic stages and its habitat. Animation is inspired from data for shell orientation in Cretaceous heteromorph ammonoids according to Kakabadzé and Sharikadzé (1993), Monks and Young (1998), Kaplan (2002). The animation will be linked with the data library PANGAEA (www.pangaea.de). Supplementary material related to this article can be found online at doi:10.1016/j.cageo.2012.04.003.

3D visualisation of ontogenetical stages in Dissimilites

Although the presented animation is based on the best preserved and most complete specimen known, the embryonic stage is still unknown (Lukeneder and Lukeneder, in press). The successive ontogenetical stages are separated into a juvenile, mid-age and adults stage (Fig. 5). Morphological terms and ontogenetical stages are in accordance to terms used by Westermann (1996), Lukeneder et al. (2010), and Lukeneder and Lukeneder (in press). The mid-aged stage herein is equivalent to the preadult stage of Klug (2001).

The resulting 3D reconstruction of ontogenetical stages in the fossil cephalopod Dissimilites appear with the juvenile cyrtocone animal (Fig. 5a), the mid-aged animal with straight shell (Fig. 5b–c) followed later by a short hook (Fig. 5d), and different views of the final, adult animal (Fig. 5e–h). The adult stage is characterised by a long, prominent hook (e.g. ancylocone) and the last change in swimming position (Animation 1).

Conclusions

The study presents results of an object-based combined analysis from computed tomography and various computed 3D facility programmes performed on the most complete shell of the fossil cephalopod Dissimilites. The first 3D visualisation of the heteromorph cephalopod genus Dissimilites from the Southern Alps (Dolomites, northern Italy) is presented. Based on the morphological changes, equivalent with changes in growth stages (e.g. ribbing, morphology and direction of shell), successive ontogenetical stages were reconstructed. Three ontogenetical stages can be separated in Dissimilites with juvenile, mid-aged and adult animals. A cyrtocone juvenile stage is followed by a straight conch, and the adult, mature stage is hooked, simultaneously accompanied by a change of swimming position. Computed tomography and palaeontological data are combined with 3D reconstructions, yielding a movie. This case study demonstrates the non-destructive possibilities of 3D visualisation for palaeontological material. The resulting images are quite realistic, and a short animated clip showing the morphology and motion of the animal is the first in such high quality using palaeontological material. The realistic 3D models and motion pictures can be simply shared amongst palaeontologists. Data, images and short-clips can be discussed online and adapted morphologically or with regard to the cephalopod's motion.