Thursday 27 October 2016

Utilising a commercial workflow when reconstructing dinosaur skeletons in 3D

Reconstructing fossils digitally has become a vital technique in palaeontology in recent years. The ability to reconstruct the entire skeletons of extinct taxa gives us the opportunity to look at aspects of an organism’s life that would prove difficult or impossible using physical models, for example in biomechanics and gait analysis.

Er, hi. The final, posed Gorgosaurus model, created in zBrush 4R7 and Cinema 4D R16.

A recent paper by Stephan Lautenschlager  ( on digital fossil restoration techniques provides a good overview of the methodology using tools available for digital palaeontology in most labs, including Avizo, Blender and Maya. I highly recommend this paper for anyone interested in the digital restoration of fossil specimens and the workflow involved, much contained in the paper being relevant to the digital reconstruction of specimens for research and outreach.

Last year I worked on a project with Dr. Willam Sellers of Animal Simulation Laboratory ( at the University of Manchester which required the creation of six accurate and complete dinosaur skeletons (see my previous post on the project:, and for this I used a workflow developed in my work creating scientific animations and illustrations for the MedComms industry, a workflow not dissimilar to many commercial studios where 3D assets of all description are produced. axon, the makers of one of the 3D modelling and animation applications I use, Cinema 4D R18, covered this project on their website:

A specimen (NHM R175) recorded using photogrammetry
and suitable for use as a basis for reconstruction of the bone.

The reference used to create individual elements comes from a number of sources. Primary amongst these are meshes generated using with photogrammetry, Lidar or CT scanning. These data are often received as point clouds that require the generation of a mesh. These datasets can be pretty hefty (especially if they are of entire mounted skeletons or other large, complex subjects) so they require chopping down into manageable chunks prior to meshing to make processing more efficient, for example isolating part of a limb or the skull. I use MeshLab ( for this part of the processes, saving sections of the point cloud and meshing them individually. The meshes generated from this procedure are the basis for the reconstruction and these are imported as reference meshes into the main 3D package prior to starting modelling. The literature was consulted and where possible collections were visited and photographs taken to maximise the available reference for modelling. This is important because as there is a fair amount of morphological variation within a particular taxa and this needs to be taken into account when modelling the skeletons, and in fact the final models are composites and don’t represent a single specimen.

Like many studios I use more than one application to create my models of palaeontological specimens. As mentioned earlier, the main 3D application I use for both research and commercial work is Cinema 4D R18 by Maxon ( Within C4D I block out the basic form of the model by generating primitives, extruding polygons and dragging edges and points into approximate position (see this post for how this works: To make these models practical for biomechanical work and 3D printing, so they needed to have as few polygons as possible whilst retaining accuracy. By starting with very simple, blocky shapes it is far easier to keep control of the polygon count as you model and make sure the mesh density is as low as possible for the final model.

Low resolution, blocked-out skull ready for importing to zBrush for further sculpting (top),
 and the skull in the process of being modelled at a higher resolution.

Once the basic shape is modelled in C4D, the meshes (both reference and model are imported into Pixologic zBrush 4R7 (, a 3D modelling package that uses sculpting in clay as a metaphor for modelling 3D meshes. Why not continue modelling in Cinema 4D or anther package? Well, zBrush’s tools are intuitive, fast and easy to use (once you’re used to them) and well suited to creating organic shapes. As a modelling tool widely used in the gaming industry zBrush also offers excellent retopologising and mesh decimation tools, which means models can have a low mesh density whilst retaining detail; it produces very ‘clean’ meshes which are perfect for importing into a wide variety of other applications. Once the model is completed the final mesh is imported back into Cinema 4D for positioning and texturing (if required). I cannot recommend zBrush highly enough for organic modelling and anyone creating reconstructions in 3D should take a close look at this package.

The skull of Gorgosaurus during the modelling process, showing the layout within zBrush 4R7.

Assembling a skeleton in Cinema 4D is a task made easier by some of the tools that are add-ons to the application and widely used by modellers and animators. Foremost amongst these is the Mograph module, which allows the cloning of a single element and the manipulation of these clones. This is tremendously useful when creating multiple copies of broadly similar elements such as vertebrae. For example, the tail several vertebrae from certain points along the sequence would be modelled and then those in between generated by cloning and these would then be adjusted individually to match the reference.

The Triceratops skeleton rigged and hot to trot in GaitSym.

The final model can be exported out as any type of 3D file, with the most useful being .obj and .fbx at present, but anticipate this changing in the future and save in several formats as well as the proprietary format of the modelling applications.

The Giraffititan model, posed.

The use of commercial tools such as zBrush is becoming more common for palaeontologists and palaeoartists, and by paying close attention to the structure of production pipelines and workflows of commercial digital studios is something we as palaeontologists should consider, as there is much to learn from their techniques and methods which we can incorporate into our own reconstruction and restoration arsenal of techniques for generating 3D meshes useful or wide variety of research pathways.

Tuesday 3 May 2016

Horshamosaurus: An enigmatic Wealden ankylosaur.

I recently visited the small but excellent museum in Horsham to take a look at one of the most enigmatic dinosaurs found in the Wealden, Horshamosaurus. Of the three species of Early Cretaceous ankylosaurs currently recognised in the English Wealden, Horshamosaurus is the least known. 
The specimen was discovered in a brickworks quarry near Rudgwick, Sussex in 1985, in the Barremian-aged rocks of the Wealden Sub-basin. Somewhat typically for Wealden dinosaur remains there is not much of it and whilst Hylaeosaurus and Polacanthus foxii are known from partial skeletons, the material representing Horshamosaurus is more fragmentary and consists of only a few elements which were found associated but disartuclated.

Dorsal vertebra of Horshamosaurus.
A) dorsal B) ventral C) right lateral D) left lateral E) anterior F) posterior

The fossils were originally assigned by British ankylosaur expert Bill Blows to Polacanthus rudgwickensis, as it displays some affinities with Polacanthus foxii, the majority of which specimens come from the Wessex Formation but with one specimen having been found in the earlier Valanginian Fm near Bexhill, Surrey. Horshamosaurus shares several synampomorphies with Polacanthus: unfused caudal chevrons, astralagus fused to the tibia and similarities in the dermal armour, but the paucity of material associated with this specimen is problematic.
There are some differences between the Rudgwick ankylosaur and Polacanthus foxii too. It's suggested that Horshamosaurus is significantly bigger than the P. foxii holotype, around 30%, but this estimate must be viewed with caution and requires further testing. It also displayed differences in vertebral morphology and the length of the tibia, plus the geological occurrence of the skeleton indicated it was not P. foxii. In his recent book Polacanthid Dinosaurs of Britain (see my review here), Blows re-assigns P. rudgwickensis to Horshamosaurus and suggests it is perhaps a nodosaurid and not a polacanthid  based on a reassessment of the character differences between it and P. foxii. Of course, the existence of a monophyletic ‘polacanthid’ clade is not settled.

Scacpulocoracoid of Horshamosaurus.
A) dorsal B) ventral C) right lateral D) left lateral E) anterior F) posterior

The main parts of the specimen consist of one complete dorsal vertebra and one broken, a couple of partial caudals of which one is a left half only, some rib sections including the proximal part of a large dorsal rib, the distal end of the scapulocoracoid, two osteoderms, the distal end of left humerus and the proximal and distal sections of the right tibia; the tibia is broken into two parts and a section of unknown length is missing. The scapulocoracoid is distinctive but the pectoral girdle of Polacanthus is poorly known, with only the Bexhill specimen and a specimen in private hands having part of the scapular preserved, however this appears to be less robust than Horshamosaurus. The Horshamosaurus scapular and coracoid are fused, this condition is not known to be a characteristic of Polacanthus as the coracoids of all the other published specimens are missing..
Of the two osteoderms preserved, one is a partial roof-like, thin-walled osteoderm, the other a large keeled osteoderm with a solid base. In his 1996 paper describing the specimen Blows suggests that the thin-walled osteoderm might be indicative of an ankylsoaurid affinity for this animal; there is some support for the taxonomic utility of ankylosaur osteoderms so this could be significant but as this is not a commonly seen morphology in Wealden ankylosaurs a larger sample size of these osteoderms  is needed.

Horsham museums's dinosaur display cabinet, with Horshamosaurus on the white wall on the right.

The reassignment of Horshamosaurus by Blows in his 2015 book is tentative and hopefully more remains of this enigmatic armoured dinosaur will be unearthed in due course, which will enable us to resolve it's taxonomy and shed more light on the relationships of Wealden ankylosaurs. In the meantime, if you're passing close to Horsham I can recommend dropping into the museum to see their vertebrate palaeontology collection which is small (one cabinet), but contains the world's only known Horshamosaurus.

Tuesday 12 January 2016

Walking (and making) the dinosaur

I was fortunate enough to work on a fascinating project last year led by Dr. Bill Sellers from the University of Manchester and which was published as a Peer-J preprint just before Christmas. The full preprint is available here:

Dr. Sellers has been working on the biomechanics of dinosaurs and other tetrapods for several years and has developed an application called GaitSym that calculates walking or running gaits, testing walk cycles until the program finds the most efficient which can help form a hypothesis to be formed on how an animal might have moved around. GaitSym requires 3D skeletal data in the form of scans or models that are then rigged with muscles that allow the simulation to calculate the forward dynamics.

Dr Sellers then built a new version of GaitSym that allows people to control dinosaurs themselves. By replacing the algorithms that calculate forward dynamics with an external control system, in this case a Kinect for Xbox wired up to a Windows PC, a person standing a few feet away can control the rigged dinosaur on the screen, enabling it to walk, run or dance.

Triceratops skeleton rigged with virtual muscles in GaitSymKinect.
Image courtesy of Dr. William Sellers.

The software created by Dr. Sellers that allows people to control these dinosaur skeletons is called GaitSymKinect. The dinosaur skeletons are rigged as we think they would be in life and GaitSymKinect translates the movements of the user into movement for the dinosaurs, allowing a person to make Tyrannosaurus rex do the Charleston, or a Triceratops gallop. The system was tested last year at the Cheltenham Science Festival and is now freely available, along with the dinosaur skeletons to go with it, follow this link here:

My part was to create the dinosaur skeletons to be used in GaitSymKinect whilst also making them suitable for being made freely available for 3D printing and just about anything else a 3D mesh can be used for. The skeletons were created to be as accurate as possible whilst not representing an actual specimen; scans, photogrammetry and the literature were all sources referred to when creating the skeletons. They are not detailed down to the smallest foramen in order to keep the polygon count as low as possible but they are accurate and would be useful for adapting to specific specimens if required and were created in Maxon Cinema 4D R16 and zBrush 4R7.

Six complete skeletons were created: Tyrannosaurus, Gorgosaurus, Triceratops, Edmontosaurus, Brachiosaurus and Edmontia. The final skeletal models are ideal for biomechanical work, adding to artworks and of course 3D printing. All this and they are free, released under CC-BY The dinosaurs skeletons modelled are shown below. If you do use them for anything, it’d be great if you could show us what you’ve done with them.

The six dinosaur skeletons built as 3D meshes and available for free download.
Clicking should embiggen.


Sellers WI, Pond SB. (2015) Kinect controlled dinosaur simulations for education and public outreach. PeerJ PrePrints 3:e1979