A palaeobiologist's guide to 'virtual' micro-CT preparation

Abstract

This paper provides a brief but comprehensive guide to creating, preparing and dissecting a ‘virtual’ fossil, using a worked example to demonstrate some standard data processing techniques. Computed tomography (CT) is a 3D imaging modality for producing ‘virtual’ models of an object on a computer. In the last decade, CT technology has greatly improved, allowing bigger and denser objects to be scanned increasingly rapidly. The technique has now reached a stage where systems can facilitate large-scale, non-destructive comparative studies of extinct fossils and their living relatives. Consequently the main limiting factor in CT-based analyses is no longer scanning, but the hurdles of data processing (see disclaimer). The latter comprises the techniques required to convert a 3D CT volume (stack of digital slices) into a virtual image of the fossil that can be prepared (separated) from the matrix and ‘dissected’ into its anatomical parts. This technique can be applied to specimens or part of specimens embedded in the rock matrix that until now have been otherwise impossible to visualise. This paper presents a suggested workflow explaining the steps required, using as example a fossil tooth of Sphenacanthus hybodoides (Egerton), a shark from the Late Carboniferous of England. The original NHMUK copyrighted CT slice stack can be downloaded for practice of the described techniques, which include segmentation, rendering, movie animation, stereo-anaglyphy, data storage and dissemination. Fragile, rare specimens and type materials in university and museum collections can therefore be virtually processed for a variety of purposes, including virtual loans, website illustrations, publications and digital collections. Micro-CT and other 3D imaging techniques are increasingly utilized to facilitate data sharing among scientists and on education and outreach projects. Hence there is the potential to usher in a new era of global scientific collaboration and public communication using specimens in museum collections. Richard Leslie Abel, MSK Laboratory, Department of Surgery and Cancer, Charring Cross Hospital, Imperial College, W6 8RF London, United Kingdom. richard.abel@imperil.ac.uk and Image and Analysis Centre, Mineralogy Department, Natural History Museum, Cromwell Road, SW7 5BD London, United Kingdom. Carolina Rettondini Laurini, Laboratorio de Paleontologia Departamento de Biologia FFCLRP USP, Av. Bandeirantes, 3900 CEP 14040-901, Bairro Monte Alegre, Ribeirao Preto, SP, Brazil. xirra.carolina@gmail.com PE Article Number: 15.2.6T Copyright: Palaeontological Association May 2012 Submission: 12 May 2011. Acceptance: 25 April 2012 Abel, Richard Leslie, Laurini, Carolina Rettondini, and Richter, Martha 2012. A palaeobiologist’s guide to ‘virtual’ micro-CT preparation. Palaeontologia Electronica Vol. 15, Issue 2;6T,17p; palaeo-electronica.org/content/issue-2-2012-technical-articles/233-micro-ct-workflow ABEL ET AL.: MICRO-CT WORKFLOW Martha Richter, Department of Palaeontology, Natural History Museum, Cromwell Road, SW7 5BD London, United Kingdom. m.richter@nhm.ac.uk