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Homogenization of sample absorption for the imaging of large and dense fossils with synchrotron microtomography

Nature Protocols volume 8, pages 1708–1717 (2013)Cite this article

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Abstract

Propagation phase-contrast synchrotron radiation microtomography (PPC-SRμCT) has proved to be very successful for examining fossils. Because fossils range widely in taphonomic preservation, size, shape and density, X-ray computed tomography protocols are constantly being developed and refined. Here we present a 1-h procedure that combines a filtered high-energy polychromatic beam with long-distance PPC-SRμCT (sample to detector: 4–16 m) and an attenuation protocol normalizing the absorption profile (tested on 13-cm-thick and 5.242 g cm−3 locally dense samples but applicable to 20-cm-thick samples). This approach provides high-quality imaging results, which show marked improvement relative to results from images obtained without the attenuation protocol in apparent transmission, contrast and signal-to-noise ratio. The attenuation protocol involves immersing samples in a tube filled with aluminum or glass balls in association with a U-shaped aluminum profiler. This technique therefore provides access to a larger dynamic range of the detector used for tomographic reconstruction. This protocol homogenizes beam-hardening artifacts, thereby rendering it effective for use with conventional μCT scanners.

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Figure 1: Illustration of the principle of normalization of the absorption profile.
Figure 2: Setup for imaging acquisition in conditions of PPC-SRμCT and normalization of the absorption profile.
Figure 3: Calculated energy spectra adjusted to different samples.
Figure 4: The photograph on the left shows the dense fossil sample that was imaged using PPC-SRμCT with the attenuation protocol (Ichthyostega thorax).
Figure 5: The photographs at the top of the figure show each side if the nodule, thereby exhibiting the fossil that is imaged in the following tomograms (A.C1870-479-4B, MNHN).
Figure 6: Design of the profiler and attenuator.
Figure 7

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Acknowledgements

We acknowledge the ESRF for access to beamlines ID19 and ID17 (in-house beam time; proposals EC521, EC685), as well as R. Able (National History Museum, London), C. Martin (University of Manchester) and A. Heaver (University of Cambridge) for access to microtomography scanning equipment in their care. We thank J.-S. Steyer (Centre National de la Recherche Scientifique–Muséum National d'Histoire Naturelle, Paris) for providing fossil material for comparative tests. S.S. is supported by European Research Council grant 233111 (P.E. Ahlberg). V.F. is supported by a University Research Committee grant, University of the Witwatersrand. S.E.P. is supported by UK Natural Environment Research Council grants NEG0058771 and NEG00711X1 (J.A. Clack and J.R. Hutchinson).

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Authors and Affiliations

  1. European Synchrotron Radiation Facility (ESRF), Grenoble, France

    Sophie Sanchez, Vincent Fernandez & Paul Tafforeau

  2. Subdepartment of Evolution and Development, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden

    Sophie Sanchez

  3. Bernard Price Institute (BPI) for Palaeontological Research, University of the Witwatersrand, Johannesburg, South Africa

    Vincent Fernandez

  4. Department of Zoology, University Museum of Zoology, University of Cambridge, Cambridge, UK

    Stephanie E Pierce

  5. Department of Veterinary Basic Sciences and Structure and Motion Laboratory, The Royal Veterinary College, Hatfield, UK

    Stephanie E Pierce

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  1. Sophie Sanchez
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  2. Vincent Fernandez
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Contributions

P.T. developed the concept, designed the protocol, conducted several experiments (including EC521) and contributed to the figures and writing of the manuscript. S.S. and P.T. conducted the experiments for EC685 (with assistance from S.E.P for specimen setup). S.S. wrote the manuscript and contributed to the figures. V.F. participated in initiating the protocol and performing a PPC-SRμCT comparative experiment, and contributed to the figures and writing of the manuscript. S.E.P. conducted the μCT comparative experiments and contributed to the figures and writing of the manuscript.

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Correspondence to Sophie Sanchez.

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Sanchez, S., Fernandez, V., Pierce, S. et al. Homogenization of sample absorption for the imaging of large and dense fossils with synchrotron microtomography. Nat Protoc 8, 1708–1717 (2013). https://doi.org/10.1038/nprot.2013.098

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