Reproducible Digital Restoration of Fossils Using Blender

Abstract

Digital restoration of fossils based on computed tomographic (CT) imaging and other scanning technologies has become routine in paleontology. Digital restoration includes the retrodeformation and reconstruction of a fossil specimen. The former involves modification of the original 3D model to reverse post-mortem brittle and plastic deformation; and the latter involves the infilling of fractures, addition of missing pieces, and smoothing of the mesh surface. The restoration process often involves digital editing of the specimen in ways that are difficult to document and reproduce. To record all actions taken during the digital restoration of a fossil, we outline a workflow that generates both the restored bone and the sequence of steps involved in its retrodeformation and reconstruction. Our method can also generate an animation showing the transformation of the original digital model into its final form. We applied this method to a dorsal rib and frontal bone of a small-bodied Jurassic-age armored dinosaur from Africa, the digital restoration of which engaged all modalities of deformation (translation, rotation, scaling, distortion) and reconstruction (fracture infilling, adding missing bone, surface smoothing). Each bone was CT-scanned, segmented, and imported into Blender, an open-source 3D-graphics animation program. Blender has an animation tool called an “armature” that allows for precise control over portions of a surface mesh while keeping a record of manipulations. To retrodeform a fossil, an armature is created and then linked, or “rigged,” to the fossil in order to control the displacement and distortion of its fragments. After using the armature to perform retrodeformation, we use Blender to record the movement and distortion of each fragment and also record reconstructive modifications. By ensuring documentation and reproducibility in an open-source program, our workflow and output open a window onto the heretofore largely hidden process of digital restoration in paleontology.

A toolbox for the retrodeformation and muscle reconstruction of fossil specimens in Blender

“…Accuracy, automation and reproducibility are relevant concerns surrounding digital fossil restoration. There are typically very few examples of a species/element to compare the accuracy of a retrodeformed model to and methods of restoration are often poorly documented [ 5 ]. Approaches using ‘armatures’ in Blender, linked with fossil fragments and ‘posed’ to correct the displacement of fragments, offer a method to document a record of manipulations [ 5 ] through saving modifications to a ‘Pose Library’ or the production of an animation.…”

“…Similarly, methods to quantify deformation and characterize local and global deformation [ 42 ] improve the accuracy of retrodeformation by better understanding how specimens have been altered, as can explorations of the range and modes of taphonomic variation within species represented by frequent fossil specimens [ 43 ]. Figuring the extent of retrodeformation as tension maps of mesh distortions [ 5 ] or maps coloured by relative mesh distance between pre- and postretrodeformed conditions [ 44 ] present options for method documentation.…”

“…Pose —for posing character models in animation but an effective tool for moving linear structures around a pivot more accurately than the Grab or Elastic deform brushes while maintaining the shape and thickness of the area. See DeVries et al [ 5 ] for a Blender retrodeformation method focusing on posing armatures to correct long bones.…”

“…In a first step, each muscle was modelled using the new method to create a base model before further refinement. In a second step, the muscle user enters folder and file name for saving data (1) user enters muscle name (2) code creates empty with that muscle name (3) user selects bone on which muscle originates (4,5) user draws on muscle origin by selecting faces (6) code makes origin area and boundary objects (7) user selects bone on which muscle inserts (8) user draws on muscle insertion by selecting faces (8) code makes insertion area and boundary objects code matches counts in boundary loops (9), code creates muscle curve template bevels with cross section of origin (10) *if necessary*, user mirrors the cross section to match the origin (11) user adjusts tilt of curve (12) user adjusts bevel extent (13) user adjusts points of curve to get desired shape (14) code converts curve to mesh (15) user adjusts muscle mesh to match insertion (16) code bridges muscle mesh with origin and insertion (17) code resets add-on for new muscle (18) user can adjust muscle meshes iteratively (19) code calculates volumes of all muscles in scene, adds metric to .csv file (20) in above steps, code generates this hierarchy of new objects royalsocietypublishing.org/journal/rsos R. Soc. Open Sci.…”

“…9: 220519 fossil specimens [43]. Figuring the extent of retrodeformation as tension maps of mesh distortions [5] or maps coloured by relative mesh distance between pre-and postretrodeformed conditions [44] present options for method documentation.…”