Skip to main content Accessibility help

Three-Dimensional Synchrotron Virtual Paleohistology: A New Insight into the World of Fossil Bone Microstructures

  • Sophie Sanchez (a1) (a2), Per E. Ahlberg (a2), Katherine M. Trinajstic (a3) (a4), Alessandro Mirone (a1) and Paul Tafforeau (a1)...


The recent developments of phase-contrast synchrotron imaging techniques have been of great interest for paleontologists, providing three-dimensional (3D) tomographic images of anatomical structures, thereby leading to new paleobiological insights and the discovery of new species. However, until now, it has not been used on features smaller than 5–7 μm voxel size in fossil bones. Because much information is contained within the 3D histological architecture of bone, including an ontogenetic record, crucial for understanding the paleobiology of fossil species, the application of phase-contrast synchrotron tomography to bone at higher resolutions is potentially of great interest. Here we use this technique to provide new 3D insights into the submicron-scale histology of fossil and recent bones, based on the development of new pink-beam configurations, data acquisition strategies, and improved processing tools. Not only do the scans reveal by nondestructive means all of the major features of the histology at a resolution comparable to that of optical microscopy, they provide 3D information that cannot be obtained by any other method.


Corresponding author

*Corresponding author. E-mail:


Hide All
Agassiz, L. (1833–1843). Recherches sur les poissons fossiles. Neuchatel, Switzerland: Imprimerie de Petitpierre.
Ager, D.V. (1965). Serial grinding techniques. In Pages Handbook of Paleontological Techniques, Kummel, B. & Raup, D. (Eds.), pp. 212224. New York: W.H. Freeman.
Amprino, R. (1947). La structure du tissu osseux envisagée comme expression de différences dans la vitesse de l'accroissement. Arch Biol 58, 315330.
Anderson, J.S. (2007). Incorporating ontogeny into the matrix: A phylogenetic evaluation of developmental evidence for the origin of modern amphibians. In Major Transitions in Vertebrate Evolution, Anderson, J.S. & Sues, H.-D. (Eds.), pp. 182227. Bloomington, IN: Indiana University Press.
Andrews, S.M. & Westoll, T.S. (1970). The postcranial skeleton of Eusthenopteron foordi Whiteaves. T RSE Earth 68, 207329.
Bromage, T.G., Goldman, H.M., McFarlin, S.C., Perez-Ochoa, A. & Boyde, A. (2009). Confocal scanning optical microscopy of a 3-million-year-old Australopithecus afarensis femur. Scanning 31, 110.
Carlson, K.J., Stout, D., Jashashvili, T., Ruiter, D.J. de, Tafforeau, P., Carlson, K. & Berger, L.R. (2011). The Endocast of MH1, Australopithecus sediba . Science 333, 14021407.
Castanet, J., Francillon-Vieillot, H., Meunier, F.-J. & Ricqlès, A. de. (1993). Bone and individual aging. In Bone, vol. 7: Bone Growth-B, Hall, B.K. (Ed.), pp. 245283. Boca Raton, FL: CRC Press.
Cloetens, P., Ludwig, W., Baruchel, J., Van Dyck, D., Van Landuyt, J., Guigay, J.P. & Schlenker, M. (1999). Holotomography: Quantitative phase tomography with micrometer resolution using hard synchrotron radiation X rays. Appl Phys Lett 75, 29122914.
Croft, W.N. (1950). A parallel grinding instrument for the investigation of fossils by serial sections. J Paleontol 24, 693698.
Currey, J.D. (2002). Bones: Structure and Mechanics. Princeton, NJ: Princeton University Press.
Dierolf, M., Menzel, A., Thibault, P., Schneider, P., Kewish, C.M., Wepf, R., Bunk, O. & Pfeiffer, F. (2010). Ptychographic X-ray computed tomography at the nanoscale. Nature 467, 436440.
Dupret, V., Sanchez, S., Goujet, D., Tafforeau, P. & Ahlberg, P.E. (2010). Bone vascularization and growth in placoderms (Vertebrata): The example of the premedian plate of Romundina stellina Ørvig, 1975. CR Palevol 9, 369375.
Erickson, G.M., Makovicky, P.J., Currie, P.J., Norell, M.A., Yerby, S.A. & Brochu, C.A. (2004). Gigantism and comparative life-history parameters of tyrannosaurid dinosaurs. Nature 430, 772775.
Ford, B.J. (2001). The Royal Society and the microscope. Notes Rec Roy Soc 55, 2949.
Francillon-Vieillot, H., Buffrenil, V. de, Castanet, J., Géraudie, J., Meunier, F.J., Sire, J.-Y., Zylberberg, L. & Ricqlès, A. de. (1990). Microstructure and mineralization of vetebrate skeletal tissues. In Skeletal Biomineralization: Patterns, Processes and Evolutionary Trends: Volume I, Carter, J.G. (Ed.), pp. 471530. New York: Van Nostrand Reinhold.
Gross, W. (1956). Über Crossopterygier und Dipnoer aus dem baltischen Oberdevon im Zusammenhang einer vergleichenden Untersuchung des Porenkanalsystems paläozoischer Agnathen und Fische. Kungl. Svenska vetenskapsakademiens Handlingar 5, 1140.
Guigay, P., Langer, M., Boistel, R. & Cloetens, P. (2007). Mixed transfer function and transport of intensity approach for phase retrieval in the Fresnel region. Opt Lett 32, 16171619.
Hieronymus, T.L. (2006). Quantitative microanatomy of jaw muscle attachment in extant diapsids. J Morphol 267, 954967.
Irvine, S.C., Morgan, K.S., Suzuki, Y., Uesugi, K., Takeuchi, A., Paganin, D.M. & Siu, K.K.W. (2010). Assessment of the use of a diffuser in propagation-based X-ray phase contrast imaging. Opt Express 18, 1347813491.
Janvier, P. (1996). Early Vertebrates. Oxford, UK: Clarendon Press.
Jarvik, E. (1980). Basic Structure and Evolution of Vertebrates. London, UK: Academic Press.
Kiprijanoff, A.V. (1881–1883). Studien über die fossilien Reptilien Russlands. Mémoires de l'Académie Impériale des Sciences de St Petersbourg 7, 2831.
Klembara, J. & Meszároš, S. (1992). New finds of Discosauriscus austriacus (Makowsky 1876) from the Lower Permian of Boskovice Furrow (Czecho-Slovakia). Geol Carpath 43, 305312.
Lak, M., Néraudeau, D., Nel, A., Cloetens, P., Perrichot, V. & Tafforeau, P. (2008). Phase contrast X-ray synchrotron imaging: Opening access to fossil inclusions in opaque amber. Microsc Microanal 14, 251259.
Laurin, M., Meunier, F.J., Germain, D. & Lemoine, M. (2007). A microanatomical and histological study of the paired fin skeketon of the Devonian sarcopterygian Eusthenopteron foordi . J Paleontol 81, 143153.
Leeuwenhoek, A. van. (1674). Microscopical observations from Mr. Leeuwenhoek, about blood, milk, bones, the brain, spitle, cuticula, sweat, fatt, teares; communicated in two letters to the publisher. Philos T R Soc 9, 121131.
Long, J.A., Trinajstic, K. & Johanson, Z. (2009). Devonian arthrodire embryos and the origin of internal fertilization in vertebrates. Nature 457, 11241127.
Margerie, E. de, Tafforeau, P. & Rakotomanana, L. (2006). In silico evolution of functional morphology: A test on bone tissue biomechanics. J R Soc Interface 3, 679687.
Matzke-Karasz, R., Smith, R.J., Symonova, R., Miller, C.G. & Tafforeau, P. (2009). Sexual intercourse involving giant sperm in Cretaceous ostracode. Science 324, 1535.
Meunier, F.J. & Laurin, M. (2010). A microanatomical and histological study of the fin long bones of the Devonian sarcopterygian Eusthenopteron foordi . Acta Zool 81, 143153.
Organ, C.L., Shedlock, A.M., Meade, A., Pagel, M. & Edwards, S.V. (2007). Origin of avian genom size and structure in non-avian dinosaurs. Nature 446, 180184.
Owen, R. (1840–1845). Odontography, or a Treatise on the Comparative Anatomy of the Teeth, Their Physiological Relations, Mode of Development and Microscopic Structure, in the Vertebrate Animals. London, UK: Hippoly Bailliere.
Paganin, D., Mayo, S.C., Gureyev, T.E., Miller, P.R. & Wilkins, S.W. (2002). Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object. J Microsc 206, 3340.
Peyrin, F. (2009). Investigation of bone synchrotron radiation imaging: From micro to nano. Osteoporosis Int 20, 10571063.
Poplin, C. & Ricqlès, A. de. (1970). A technique of serial sectionning for the study of the undecalcified fossils. Curator 13, 720.
Pradel, A., Langer, M., Maisey, J., Geffard-Kuriyama, D., Cloetens, P., Janvier, P. & Tafforeau, P. (2009). Skull and brain of a 300 million-year-old chimaeroid fish revealed by synchrotron holotomography. P Natl Acad Sci 106, 52245228.
Ricqlès, A. de, Castanet, J. & Francillon-Vieillot, H. (2004). The “message” of bone tissue in paleoherpetology. Ital J Zool 71(Suppl 1), 312.
Rücklin, M., Giles, S., Janvier, P. & Donoghue, P.C.J. (2011). Teeth before jaws? Comparative analysis of the structure and development of the external and internal scales in the extinct jawless vertebrate Loganellia scotica. Evol Dev 13, 523532.
Ruta, M. & Coates, M.I. (2007). Dates, nodes and character conflict: Addressing the Lissamphibian origin problem. J Syst Paleontol 5, 69122.
Sansom, I.J., Smith, M.M. & Smith, P. (1996). Scales of thelodont and shark-like fishes from the Ordovician of Colorado. Nature 379, 628630.
Smith, T.M., Olejniczak, A.J., Kupczik, K., Lazzari, V., Vos, J. de, Kullmer, O., Schrenk, F., Hublin, J.-J., Jacob, T. & Tafforeau, P. (2009). Taxonomic assessment of the trinil molars using non-destructive 3D structural and development analysis. PaleoAnthropology 2009, 117129.
Smith, T.M. & Tafforeau, P. (2008). New visions of dental tissue research: Tooth development, chemistry, and structure. Evol Anthropol 17, 213226.
Smith, T.M., Tafforeau, P., Reid, D.J., Grün, R., Eggins, S., Boutakiout, M. & Hublin, J.-J. (2007). Earliest evidence of modern human life history in North African early Homo sapiens . P Natl Acad Sci 104, 61286133.
Smith, T.M., Tafforeau, P., Reid, D.J., Pouech, J., Lazzari, V., Zermeno, J.P., Guatelli-Steinberg, D., Olejniczak, A.J., Hoffman, A., Radovcic, J., Makaremi, M., Tousaint, M., Stringer, C. & Hublin, J.-J. (2010). Dental evidence for ontogenetic differences between modern humans and Neanderthals. P Natl Acad Sci 107, 2092320928.
Sollas, W.J. (1904). A method for the investigation of fossils by serial sections. T Roy Soc London B 196, 259265.
Tafforeau, P., Bentaleb, I., Jaeger, J.-J. & Martin, C. (2007). Nature of laminations and mineralization in rhinoceros enamel using histology and X-ray synchrotron microtomography: Potential implications for palaeoenvironmental isotopic studies. Palaeogeogr Palaeocl 246, 206227.
Tafforeau, P., Boistel, R., Boller, E., Bravin, A., Brunet, M., Chaimanee, Y., Cloetens, P., Feist, M., Hoszowska, J., Jaeger, J.-J., Kay, R.F., Lazzari, V., Marivaux, L., Neil, A., Nemoz, C., Thibault, X., Vignaud, P. & Zabler, S. (2006). Applications of X-ray synchrotron microtomography for non-destructive 3D studies of paleontological specimens. Appl Phys A-Mater 83, 195202.
Tafforeau, P. & Smith, T.M. (2008). Nondestructive imaging of hominoid dental microstructure using phase contrast X-ray synchrotron microtomography. J Hum Evol 54, 272278.
Witham, H.T.M. (1831). Observations on Fossil Vegetables. Edinburgh, UK: Blackwood.


Type Description Title
Supplementary materials

Sophie Sanchez et al. Supplementary Material

 PDF (1.9 MB)
1.9 MB


Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed