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SPIERS and VAXML; A software toolkit for tomographic visualisation and a format for virtual specimen interchange

Mark D. Sutton, Russell J. Garwood, David J. Siveter, and Derek J. Siveter

Plain Language Abstract

Three-dimensional (3D) fossils – especially those preserving soft tissues – are rare, but provide valuable insights into past life. Studying such specimens by splitting a rock into pieces can leave portions of the fossil embedded and place limitations on the research possible. 'Virtual palaeontology' harnesses the power of computers to create digital models of fossils, and can greatly aid fossil workers' study of 3D specimens. It is becoming an important and widespread palaeontological technique, the models generally being based on cross-sectional images evenly spaced along the length of a fossil. These can be created by sawing a fossil into sections, grinding it away, or using scanning techniques such as CT, or computed tomography. Few free software packages exist that are capable of creating digital models from such images. Software tuned to the needs of palaeontological data – which is often noisy and complex – is even rarer. Here we introduce the SPIERS software suite: a free, multi-platform, versatile and fully documented collection of programs software toolkit that can convert slice images into three-dimensional models.

As well as allowing the detailed study of 3D fossils, virtual palaeontology is a powerful tool for sharing palaeontology data (in this case, the anatomy of fossils) online, allowing fossil workers to inspect each other's work. The use of 3D models to this end has been limited to date. In part this is because palaeontologists are reluctant to share their data, but the wide range of 3D file formats and lack of any standard is another obstacle. No matter what kind of data is used to create a model, the majority of computer reconstructions end up as a mesh of triangles. Hence, to make data sharing easier, we propose a new format called VAXML. This open and transparent format relies on an existing and widely used triangle-mesh file-format, supplemented by a human-readable text (XML) file. This paper defines the format, and suggests it as a candidate for a standard file format to share virtual palaeontological and biological data. The SPIERS software suite can both read and create VAXML files; it acts as a free viewer designed to allow complex models to be loaded on relatively low-performance computers.

Resumen en Español

SPIERS y VAXML: un conjunto de herramientas de software para la visualización tomográfica y un formato para el intercambio de ejemplares virtuales

La "paleontología virtual", el estudio de los fósiles mediante modelos digitales, es una técnica paleontológica cada vez más importante. La gran mayoría de ese trabajo es tomográfico, basado en series de secciones transversales generadas físicamente o mediante técnicas de escaneo. No existen, sin embargo, paquetes de software para la reconstrucción tomográfica de uso general que estén disponibles gratuitamente y adaptados a las necesidades de los datos paleontológicos. Además de su valor en el estudio primario de los ejemplares, la paleontología virtual puede convertirse en un poderoso medio para la diseminación de datos a través de la red incrementando así en gran medida la capacidad de los paleontólogos para examinar los datos de sus colegas. Sin embargo, la ausencia de un formato estandarizado para las series de datos ha sido un impedimento mayor para el intercambio de esos datos. En este artículo proporcionamos soluciones a esos dos problemas. El paquete de software SPIERS es un conjunto de herramientas completo, gratuito, multiplataforma y plenamente documentado, para la reconstrucción de cualquier tipo de datos tomográficos en modelos tridimensionales. Aunque es capaz de realizar reconstrucciones rápidas, es especialmente adecuado para la producción de modelos cuidadosamente preparados a partir de datos difíciles. Sostenemos que la diseminación de especímenes virtuales debería hacerse mediante conjuntos de datos de mallas de triángulos que pueden generarse a partir del más amplio abanico de fuentes de datos. Por otra parte, presentamos el formato de datos VAXML como un candidato a formato estándar para la diseminación de especímenes virtuales tanto paleontológicos como biológicos. SPIERS incluye un paquete capaz tanto de visualizar como de exportar archivos VAXML, diseñado para la visualización de conjuntos complejos de datos en sistemas relativamente poco potentes.

PALABRAS CLAVE: tomografía, tridimensional, fósil virtual, infraestructura, VAXML, tomografía computarizada.

Traducción: Miguel Company

Résumé en Français

SPIERS and VAXML; un ensemble de logiciels pour la visualtion tomographique et un format pour l'accès aux specimens virtuels.

"La paléontologie virtuelle", l'étude des fossiles à travers l'utilisation de modèles digitaux, est une technique paléontologique de plus en plus importante. La grande majorité de ces travaux est fondée sur la tomographie, c'est-à-dire des jeux de données de coupes sériées quelles soient physiques ou proviennent de technologies impliquant des scanners. Cependant il n'existe pas de suites de logiciels pour les reconstitutions tomographiques qui soient gratuites et adaptées spécifiquement aux données paléontologiques. Au-delà de son potentiel dans l'étude fondamentale des spécimens, la paléontologie virtuelle peut devenir un medium puissant pour l'accès en ligne des données, augmentant considérablement la vérification par les paléontologues de leurs données respectives. L'absence de format standard pour ces jeux de données a malheureusement été un facteur limitant majeur pour leur échange. Nous présentons ici des solutions à tous ces problèmes. La suite de logiciels SPIERS comprend des outils gratuits, multi-plateforme et bien décrits pour la reconstruction de n'importe quel type de données tomographiques en modèles trois-dimensions. Dotée d'une capacité de reconstruction rapide, elle est particulièrement appropriée à la production de modèles de données difficiles préparés minutieusement. Nous proposons que l'accès aux spécimens virtuels soit rendu possible sous la forme de jeux de donées en polygones triangulaires qui peuvent être générés à partir d'un grand nombre de sources de données. Nous présentons ici le format VAXML pour ces données; ce format est un candidat pour devenir un format standard pour l'accès aux spécimens virtuels, qu'ils soient paléontologiques ou bilogiques. La suite SPIERS contient les outils capables à la fois de visualiser et d'exporter les fichiers VAXML faits pour la visualisation de jeux de données complexes sur des systèmes de puissance relativement faible.

Mots-cléfs: tomographie, trois-dimension, fossiles virtuels, infrastructure, VAXML, tomographie assistée par ordinateur.

Translator: Loïc Costeur

Deutsche Zusammenfassung

SPIERS und VAXML; Ein Software-Werkzeug für tomographische Visualisierung und ein Format für virtuellen Austausch von Stücken

„Virtuelle Paläontologie", das Untersuchen von Fossilien an digitalen Modellen ist eine paläontologische Technik die immer wichtiger wird. Die große Mehrheit solcher Arbeiten ist tomographisch und basiert auf Datensätzen von seriellen Schnitten, die entweder physikalisch oder durch Scanning-Techniken generiert wurden. Es gibt jedoch keine allgemein zugängliche, universelle Software-Pakete für tomographische Rekonstruktion, die auf die speziellen Ansprüche von paläontologischen Daten zugeschnitten sind. Zusätzlich zum Wert für das Primärstudium von Stücken hat die virtuelle Paläontologie das Potential ein mächtiges Medium für online Datenübertragung zu werden und würde damit den Grad erhöhen mit dem Paläontologen die jeweiligen Daten des anderen studieren können. Weil es jedoch keine standardisierten Datenformate für diese Datensets gab, war die Datenübertragung sehr behindert. Wir beschreiben hier Lösungen für beide Probleme. Die SPIERS-Software-Suite ist ein umfassendes, freies, Multi-Plattform und vollständig dokumentiertes Software-Werkzeug für die Rekonstruktion jeglicher tomographischen Daten zu dreidimensionalen Modellen. Sie kann eine schnelle Rekonstruktion durchführen, ist aber besonders dazu geeignet sorgfältig ausgearbeitete Modelle aus schwierigen Datensätzen zu produzieren. Wir argumentieren, dass die Verbreitung von virtuellen Stücken in Form von triangle-mesh Datensätzen, die aus einem maximal breiten Spektrum von Datenquellen generiert werden können, geschehen sollte. Wir stellen hier das VAXML Datenformat für solche Datensets vor, ein Kandidat für die Standartverbreitung von virtuellen Stücken sowohl im paläontologischen als auch biologischen Bereich. Das SPIERS-Suite - Paket kann VAXML-Dateien visualisieren und exportieren und ist so gestaltet, dass komplexe Datensätze auch mit Systemen mit relativ geringer Leistung gesehen werden können.

KEY WORDS: Tomographie, dreidimensional, virtuelle Fossilien, Infrastruktur, VAXML, Computertomograpie

Translators: Eva Gebauer and Anke Konietzka

Arabic

289 arab

Translator: Ashraf M.T. Elewa

Polski Abstrakt

SPIERS I VAXML, OPROGRAMOWANIE DO WIZUALIZACJI I FORMAT DO WIRTUALNEJ WYMIANY GATUNKÓW

„Paleontologia wirtualna", badanie skamieniałości przy wykorzystaniu modeli cyfrowych, jest dynamicznie rozwijającą się metodą w paleontologii. Ogromną większość analiz stanowi tomografia opierająca się na serii wycinków danego obiektu generowanych w świecie rzeczywistym lub poprzez skanowanie. Nie ma niestety oprogramowania ogólnego zastosowania do rekonstrukcji tomograficznych dostępnego za darmo i dostosowanego do potrzeb danych paleontologicznych. Oprócz znaczenia dla podstawowego badania okazów, paleontologia wirtualna ma potencjał by stać się potężnym medium do dzielenia się danymi paleontologicznymi poprzez internet, zwiększając możliwości przeglądania baz danych różnych paleontologów. Jednakże brak ustandaryzowanego formatu dla tych baz danych jest podstawowym czynnikiem powstrzymującym wymianę danych. W artykule opisujemy rozwiązanie dla obu tych problemów. SPIERS jest kompletnym, darmowym, wieloplatformowym pakietem oprogramowania z pełną dokumentacją służącym do rekonstrukcji jakichkolwiek danych tomograficznych do modeli 3D. Oprócz możliwości tworzenia szybkich rekonstrukcji, oprogramowanie jest szczególnie przydatne do tworzenia dokładnych modeli ze skomplikowanych baz danych. Proponujemy aby dzielenie się wirtualnymi okazami odbywało się przy pomocy baz danych opartych na trójkątnej siatce, które mogły by być generowane z maksymalnie szerokiego zakresu źródeł danych. Przedstawiamy format VAXML dla tego typu baz danych, kandydata na standardowy format dla okazów wirtualnych, zarówno paleontologicznych jak i biologicznych. Oprogramowanie SPIERS zawiera pakiet zdolny zarówno do wizualizacji jak i eksportu plików VAXML, zaprojektowany do odczytywania skomplikowanych baz danych na systemach o słabej wydajności.

Słowa kluczowe: tomografia, 3D, wirtualne skamieniałości, infrastruktura, VAXML, tomografia komputerowa

Translators: Dawid Mazurek, Robert Bronowicz, and Daniel Madzia

 

Anke Konietzka
 

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Department of Earth Science and Engineering
Mark SuttonSouth Kensington Campus
Imperial College
London SW7 2AZ
United Kingdom
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Mark Sutton is a Senior Lecturer in Palaeontology at Imperial College, London. He studied at Cambridge (undergraduate) and Cardiff (PhD), and has held academic appointments at Lampeter, Oxford and, since 2005, Imperial College, London. His research has primarily centered around the three-dimensionally preseved invertebrate fossils of the Silurian ‘Herefordshire Lagerstätte’, but he maintains broad interests in the phylogeny and evolution of many groups, particularly the brachiopods, arthropods and molluscs. His research interests also include computer-applications in Palaeontology, especially three-dimensional reconstruction techniques. He is married with two children, and lives in Oxfordshire.

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Manchester X-ray Imaging Facility
Russell GarwoodSchool of Materials
The University of Manchester
Oxford Rd.,
Manchester M13 9PL
United Kingdom

Russell Garwood is currently a research associate in 3D and 4D geological materials imaging, based at the Research Complex at Harwell (Rutherford Appleton Laboratory, Didcot) and part of the Manchester X-Ray Imaging Facility. He studied at Imperial College, London as an undergraduate, and a PhD student, completing a thesis on the 3D reconstruction of Carboniferous fossils in Late 2010. His research to date has focused on the palaeobiology of early terrestrial arthropods as revealed by CT scanning and computer reconstruction. More recently he has acted as the computed tomography lab manager at the Natural History Museum, London, which has allowed him to apply the same techniques to a wide range of geological, mineralogical, palaeontological, archaeological and historical problems. His other research interests include the computer modelling of evolution, abiogenesis, and early evolution.

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Department of Geology, Bennett Building
University of Leicester
University Road
Leicester, LE1 7RH
United Kingdom

David Siveter is Emeritus Professor of Palaeontology at the University of Leicester. He read for his BSc and doctorate at Leicester and has subsequently held academic appointments at his Alma Mater. His research interests are in Palaeozoic stratigraphy and palaeontology, especially ostracods and other arthropods. Much of his work has been to elucidate the stratigraphical and biogeographical utility of ostracods, their ecological radiation, especially the origin of pelagic lifestyles, and how evidence from exceptionally well preserved fossils has shed light on the origin and evolution of the group. Europe, North America, Russia, central Asia and China are his main fieldwork areas. His current research focuses on arthropod-bearing Konservat-Lagerstätten from the Cambrian and Silurian.

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Derek SiveterUniversity Museum of Natural History & Department of Earth Sciences
University of Oxford
Parks Road
Oxford, Manchester OX1 3PR
United Kingdom

Derek Siveter gained a BSc, PhD. (Ordovician to Devonian trilobites from NW Europe) and DSc from the University of Leicester. He held positions at Trinity College, Dublin and the University of Hull, and then for approaching 25 years, at the University of Oxford, where in 2011 he retired as Curator of Geology in the University Museum of Natural History, and Professor in Earth Sciences. Currently he is an Honorary Research Associate of the Oxford University Museum, and Professor Emeritus of the university. Fossil arthropods and Lower Palaeozoic (especially Silurian) geology have been central to his research interests. In the last 15-20 years he has also investigated the preservation, palaeobiology, systematics and evolutionary significance of animals of the Herefordshire (Silurian) Lagerstätte, and also the Chengjiang (Cambrian) Lagerstätte in Yunnan Province, China.

 

TABLE 1. Advantages and disadvantages of STL, PLY, DXF, 3DS, VRML/X3D and PDF/U3D file formats as candidate virtual palaeontology dissemination formats.

Name Advantages Problems
STL & PLY Simple file format, widely used and understood by almost all software. Two subtypes – human readable (ASCII) format, computer readable (binary) format. No capacity for multiple objects; no capacity for storage of metadata; ASCII STL files are very large; binary files smaller but lack compression facilities. STL files cannot store vertex colour information. PLY files can include non-standard attributes.
DXF Simple file format, widely used and understood by most software. Human readable. Multiple named objects supported. Files typically very large (larger than STL); very limited facilities to store approriate metadata (limited to names essentially - no facility to correctly represent colour of objects for instance).
3DS Flexible format, compact, allows for some accompanying metadata. Limit of 65536 triangles per mesh; lacks facilities for abitrary metadata tagging of objects; not human readable.
VRML/X3D Widely used format, though not as extensively so as STL and DXF; VRML (older iteration) human readable, some metadata facilities; X3D provides more compact binary files at expense of human readability. VRML files in particular typically very large (larger than DXF); viewing software relatively low performance (and X3D software scarce), do not scale well to large triangle-count models; lack facilities for abitrary metadata tagging of objects.
PDF/U3D 3D PDFs (incorporating U3D) data can be viewed in free Adobe Reader software, already deployed to the bulk of computers; good metadata facilities; relatively small file sizes Limited range of viewing software (limited essentially to Adobe Reader) that lacks key facilities (e.g. stereo-viewing), does not support export of data, and is unproven for large triangle count models; lack of free export tools to generate files; lack of transparency and human readability in file format.

 

FIGURE 1. Workflow in SPIERS.

figure1

FIGURE 2. Virtual palaeontology workflows; arrows represent processes, rectangular boxes represent datasets, and ovals represent outputs.

figure2

 

All appendixes are zipped into this downloadable file.

APPENDIX 1. VAXML Specification

APPENDIX 2. VAXML Samples

APPENDIX 3. Manual for SPIERSedit (version 2.13)

APPENDIX 4. Manual for SPIERSview (version 2.13)

APPENDIX 5. Manual for SPIERSalign (version 2.13)