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C. R. Palevol 9 (2010) 361–368
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General palaeontology
Synchrotron X-ray imaging of inclusions in amber
Imagerie par rayonnement X synchrotron d’inclusions dans l’ambre
Carmen Soriano a,b,∗ , Mike Archer c , Dany Azar d,e , Phil Creaser c , Xavier Delclòs f ,
Henk Godthelp c , Suzanne Hand c , Allan Jones g , André Nel e , Didier Néraudeau b ,
Jaime Ortega-Blanco f , Ricardo Pérez-de la Fuente f , Vincent Perrichot b ,
Erin Saupe h , Mónica Solórzano Kraemer i,j , Paul Tafforeau a
a
European Synchrotron Radiation Facility - X-Ray Imaging Group, 6, rue Jules-Horowitz, 38000 Grenoble, France
CNRS UMR 6118, géosciences & observatoire des sciences de l’université de Rennes, université Rennes 1, campus de Beaulieu, 35042 Rennes, France
c
School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney 2052, Australia
d
Lebanese University, P.O. Box 26110217, Fanar-Matn, Lebanon
e
CNRS UMR 7205, Muséum national d’histoire naturelle, 75231 Paris, France
f
Facultat de Geologia, Universitat de Barcelona, Barcelona 08024, Spain
g
Australian Key Centre for Microscopy & Microanalysis, University of Sydney, Sydney 2006, Australia
h
University of Kansas, Lawrence-Kansas 66045, USA
i
Steinmann Institut für Geologie, Mineralogie und Paläontologie, Bonn 53115, Germany
j
Senckenberg Forschungsinstitut und Naturmuseum, Frankfurt am Main 60325, Germany
b
a r t i c l e
i n f o
Article history:
Received 2 March 2010
Accepted after revision 29 July 2010
Available online 29 October 2010
Written on invitation of the Editorial Board
Keywords:
Amber
Synchrotron phase contrast X-ray imaging
3D reconstruction
Microtomography
a b s t r a c t
Over the past six years, organic inclusions preserved in amber samples from outcrops worldwide have been discovered and imaged in 3D using propagation phase contrast based X-ray
synchrotron imaging techniques at the European Synchrotron Radiation Facility (ESRF). A
brief description of the techniques and protocols used for detecting and 3D non-destructive
imaging of amber inclusions is provided. The latest results from the major amber projects
in the ESRF are given, illustrating the increasing utility of the imaging capabilities of X-ray
synchrotron phase contrast microtomography.
© 2010 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.
r é s u m é
Mots clés :
Ambre
Imagerie par rayonnements X Synchrotron
en contraste de phase
Reconstruction 3D
Microtomographie
Au cours des six dernières années, de nombreuses inclusions d’organismes préservés dans
des ambres d’origines géographiques diverses ont été imagées en trois dimensions, voire
découvertes, grâce à la microtomographie à haute résolution en contraste de phase à
rayonnement X synchrotron, à l’Installation Européenne de Rayonnement Synchrotron
(ESRF, Grenoble, France). Une brève description des techniques et protocoles utilisés pour
la détection et l’imagerie 3D non destructive des inclusions de l’ambre est fournie. Les
∗ Corresponding author.
E-mail addresses: carmen.soriano@gmail.com, carmen.soriano@esrf.fr (C. Soriano), m.archer@unsw.edu.au (M. Archer), azar@mnhn.fr (D. Azar),
philcreaser@grapevine.com.au (P. Creaser), xdelclos@ub.edu (X. Delclòs), h.godthelp@unsw.edu.au (H. Godthelp), s.hand@unsw.edu.au (S. Hand),
allan.jones@sydney.edu.au (A. Jones), anel@mnhn.fr (A. Nel), didier.neraudeau@univ-rennes1.fr (D. Néraudeau), j.ortegablanco@ub.edu (J. Ortega-Blanco),
perezdelafuente@ub.edu (R. Pérez-de la Fuente), vincent.perrichot@univ-rennes1.fr (V. Perrichot), eesaupe@ku.edu (E. Saupe),
msolorzanokraemer@gmail.com (M.S. Kraemer), tafforeau@esrf.fr (P. Tafforeau).
1631-0683/$ – see front matter © 2010 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.
doi:10.1016/j.crpv.2010.07.014
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C. Soriano et al. / C. R. Palevol 9 (2010) 361–368
derniers résultats des principaux projets engagés sur l’ambre à l’ESRF présentés ici montrent
l’intérêt croissant des possibilités d’imagerie par microtomographie en rayonnements X
synchrotron.
© 2010 Académie des sciences. Publié par Elsevier Masson SAS. Tous droits réservés.
1. Introduction
Amber results from the fossilization of various tree
resins and is found in sediments dating from the Paleozoic to Holocene. Although the oldest ambers with
biological remains (microorganisms) date from the Triassic (Schmidt et al., 2006), macroinclusions have not
been found in sediments older than the Lower Cretaceous
(c.a. Grimaldi and Engel, 2005; Martínez-Delclòs et al.,
2004). Due to the exceptional preservation of organisms
in amber, these Lagerstätten often preserve a significant
part of the ecosystems in which the amber-producing
trees lived. Further, ethological behaviour may be captured (such as evidence of phoresis or parasitism). Various
studies have demonstrated that it is possible to obtain
information about the soft anatomy of organisms preserved in amber (Grimaldi et al., 1994; Penney et al., 2007;
Poinar and Hess, 1982), although most of these techniques
led to the destruction of the sample (e.g. Grimaldi et al.,
1994).
Amber opacity varies greatly among deposits and
between samples from the same outcrop. In some cases,
the transparency of the resin is high enough to allow
the study of the inclusions by classical optic methods
(binocular, electronic and confocal microscopes). However, in other cases, the inclusions may be obscured
by amber impurities, white foams (due to presence
of microbubbles) or oxidation or hydration processes
(Martínez-Delclòs et al., 2004), greatly decreasing access
to anatomical data of the animal or plant preserved
in the resin. In extreme cases, the amber pieces are
completely opaque, making it virtually impossible to
recognize the presence of inclusions inside (MartínezDelclòs et al., 2004; Perrichot, 2004). Recently, a new
approach for studying amber inclusions within opaque
pieces was published, namely X-ray synchrotron radiation using phase propagation contrast (Tafforeau et al.,
2006). This technique was later optimized and applied to a
large quantity of opaque French Lower Cretaceous amber
material from Charentes (Lak et al., 2008a, 2008b), establishing the basis for the study of amber with synchrotron
radiation and its later application to different ambers
worldwide.
2. Methods
Using third generation synchrotrons, it is possible to
obtain a partially coherent X-ray beam due to the small
source size and the long distance between the source
and the sample (140 meters in the case of the ESRF
ID19 beamline). As a result of the coherence, interfaces
in the sample create interferential pattern propagation
in space. It is then possible to detect enhanced contrast of the sample interfaces just by increasing the
distance between the sample and the detector (propagation phase contrast effect). Since the phase contrast
effect is far more sensitive than the absorption one, the
technique allows for detection of inclusions that would
have remained invisible using only absorption contrast
(Lak et al., 2008a, 2008b; Tafforeau et al. 2006). This
property can be also achieved in some conventional microtomographic devices, but only in small samples at high
resolution and low energy (Penney et al., 2007). Nowadays, propagation phase contrast is the most frequently
used technique for high-resolution tomographies of inclusions in amber (chiefly performed at the ESRF), with voxel
size ranging from 0.35 to 15 m in the case of larger samples.
The success of the first study (Tafforeau et al., 2006)
prompted further development of X-ray synchrotron imaging for other amber inclusions and deposits (e.g., Lak et
al., 2008a). Eighty percent of French Cretaceous amber
pieces are opaque (Perrichot, 2004), and as such, it is often
difficult to know whether there are inclusions within a
given piece. To combat this, Lak et al. (2008b) used optimized phase contrast-based microradiographic protocol
to survey large quantities of opaque pieces for possible inclusions. Amber pieces were immersed in water to
optimize the phase contrast effect by reducing the relative residual absorption contrast. The microradiographs
of the opaque blocks were normalized and then surveyed
at real resolution size to look for inclusions. Later, select
specimens were imaged by propagation phase contrast
X-ray synchrotron microtomography (PPC-SRCT) using
local tomography protocol (the amber block being, in most
of the cases, far larger than the inclusion itself). Energy
was adapted depending upon the size and density pattern of the amber blocks (i.e. presence of pyrite requiring
higher energy). Resolution was selected to optimize the
level of detail necessary for each inclusion. In some cases,
we used a multiscale approach, starting with a complete
block tomography (when containing several organisms),
followed by detailed scans of selected inclusions, and finishing with higher resolution scans of diagnostic parts of
these inclusions.
Using this method of microradiographic survey and
later microtomography, more than 350 specimens were
recognized inside the blocks of opaque amber from
France, thus opening a new window for palaeoentomology.
After acquisition of the scans, the volumes are
reconstructed using a filtered back-projection algorithm
adapted for local tomography applications (PyHST software, ESRF). The later 3D processing is performed
on powerful workstations using the software VGStudioMax (Volume Graphics, Heidelberg, Germany). The
segmentation protocol, which virtually extracts the
organisms, is based on controlled 3D region growing, fol-
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Fig. 1. 3D reconstructions of Lower Cretaceous French amber insects using PPC-SRCT at ID19 beamline, ESRF, Grenoble. 1: Coleopteran larva, specimen
MNHN A33496 (ARC-331.5), voxel size 0.55 m, propagation distance 70 mm, 35 keV, scale bar 500 m. 2: Raphidiopteran pupa, specimen MNHN A33497
(ARC-332.1), voxel size 7.46 m, propagation distance 800 mm, 25 keV, scale bar 5 mm.
Fig. 1. Reconstructions 3D d’insectes dans l’ambre Crétacé inférieur de France, effectuées par PPC-SRCT sur la ligne de lumière ID19, ESRF, Grenoble. 1 :
Larve de Coléoptère, spécimen MNHN A33496 (ARC-331.5), taille de pixel 0,55 m, distance de propagation 70 mm, 35 keV, barre d’échelle 500 m. 2 :
Pupe de Raphidioptère, spécimen MNHN A33497 (ARC-332.1), taille de pixel 7,46 m, distance de propagation 800 mm, 25 keV, barre d’échelle 5 mm.
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Fig. 2. 3D reconstruction of a monotomid beetle (Rhizophtoma elateroides Kirejtshuk et al., 2009), specimen 1512, Coll. D. Azar, from Lower Cretaceous
Lebanese amber using PPC-SRCT at BM05 beamline, ESRF, Grenoble. Voxel size 1.03 m, propagation distance 50 mm, 20.5 keV. Scale bar 500 m.
Fig. 2. Reconstruction 3D d’un Coléoptère Monotomidé (Rhizophtoma elateroides Kirejtshuk et al., 2009), spécimen 1512, Coll. D. Azar, dans l’ambre Crétacé
inférieur du Liban, effectuée par PPC-SRCT sur la ligne de lumière BM05, ESRF, Grenoble. Taille de pixel 1,03 m, distance de propagation 50 mm, 20,5 keV.
Barre d’échelle 500 m.
lowed by manual refinement of the rough first result
(Fig. 1).
After publication of an exemplar, the microtomographic
data is available online in the free access paleontological database at http://paleo.esrf.eu, including original
reconstructions of the scan, all the scan parameters,
the segmented slices, the VGStudioMax files, .stl surface files for 3D printing, plates and animations with
anaglyphic versions. When possible, 3D prints in ABS plus
plastic are constructed at the ESRF, which are used as
accessible physical representations of the virtual holotypes.
The specimens included in these publications are
deposited in the following institutions: French and
Lebanese amber at the Division of Palaeontology of
the Natural History Museum of Paris (MNHN, France),
with French amber being provisionally housed at the
Geological Department of the University of Rennes
1 (France); Spanish amber in the Fundación Conjunto Paleontológico Dinopolis (CPT) and in the Museo
de Ciencias Nacional de Alava (MCNA), Spain; and
Australian amber at the Queensland Museum (Australia).
3. Results
In the last 6 years, amber pieces from virtually the
world over have been scanned or surveyed in the ESRF,
but long-term projects have been launched only with
amber collections from the Cretaceous of France, Spain, and
Lebanon, and from the Tertiary of Australia.
The French Cretaceous amber material was the first to
be surveyed and microtomographied by synchrotron Xray imaging (Lak et al., 2008b; Tafforeau et al., 2006), and
since the beginning of this work, several hundred plant and
animal specimens have been recognized. The French Cretaceous amber outcrops are located mainly in the Southwest
of France, and their ages range from Albian to Cenomanian
(Néraudeau et al., 2002, 2003, 2005, 2008, 2009; Perrichot
and Néraudeau, 2009; Perrichot et al., 2007, 2010).
As noted, the large quantity of opaque amber pieces
(approximately 80%) from the Lower Cretaceous French
material spurred study using X-ray synchrotron microtomography (Lak et al., 2008a, 2008b). Because synchrotron
imaging was first applied to the French deposit, the material has, at this stage, been reconstructed in 3D and
published most extensively (Lak et al., 2008b, 2009; Lak
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Fig. 3. Coleoptera (Nemonychidae), specimen CPT-4106, from the Lower
Cretaceous Spanish amber. 1: Photography of the specimen with
binocular. 2: 3D reconstruction of the complete body. 3: Transverse plane
projection, showing the hind wings folded (a) and preserved under the
elytra (b) and digestive tract (c).
Fig. 3. Coléoptère (Nemonychidae), spécimen CPT-4106, dans l’ambre
Crétacé inférieur d’Espagne. 1 : Photo du spécimen à la loupe binoculaire.
2 : Reconstruction 3D du corps complet. 3 : Projection transverse plane
montrant les ailes postérieures pliées (a) et préservées sous les élytres (b)
et le tube digestif (c).
and Nel, 2009; Perrichot et al., 2008; Tafforeau et al., 2006;
Vršanský, 2009).
The latest discoveries from these amber deposits
include different larval stages of various groups of insects,
including coleopterans and raphidiopterans (Fig. 1). Formal systematic study of these inclusions is complicated
because the larval stages of these families do not resemble the adult stages, but they may contribute to the
general ecosystem reconstruction. Data from the specimens are available online on the ESRF paleontological
database described above. Furthermore, a great number of
365
new larval and adult forms of dipterans, coleopterans, heteropterans, hymenopterans and other groups are currently
under study.
Following the success of the French pilot study in late
2008, work began on the Lower Cretaceous amber collection from Lebanon using PPC-SRCT at the ESRF. Until now,
the Lebanese amber deposits, with more than 300 outcrops,
are considered to be the oldest with arthropod inclusions
(Azar, 2007), and so far numerous representatives of different groups of arthropods, vertebrates and plants have
been recognized. Although the amber is fairly transparent,
some pieces were surveyed by microtomography to study
the internal features of the inclusions and/or to resolve
anatomical details invisible with conventional techniques
(as was the case, for example, for the oldest representative
of the beetle family Monotomidae) (Fig. 2) (Kirejtshuk et
al., 2009).
In 2009, a new project studying the fossil content
of the Spanish amber outcrops began, and approximately one hundred specimens have already been scanned
on the ID19 and BM05 beamlines of the ESRF using
PPC-SRCT. The Spanish amber dates from the BarremianCenomanian. The first outcrop with paleobiological content
was described in 2000 from Albian deposits (Alonso et
al., 2000), and since then several outcrops have been discovered that yield a rich collection of animals and plants
(Delclòs et al., 2007; Peñalver et al., 2007; Najarro et al.,
2009).
Spanish amber samples are generally translucent, so Xray synchrotron microradiographic techniques to detect
inclusions are not needed. Even so, partial opacity of samples and/or debris within a piece can make the study of
morphological details extremely difficult (Fig. 3). In other
cases, data on the internal anatomy is required to perform a thorough systematic study. The preservation of
internal structures in some Spanish samples has allowed
for unprecedented, exhaustive study of the inclusions,
for example making it possible to see the hind wings
underneath the elytra of beetles (Fig. 3). Other Spanish specimens that have been reconstructed include a
female spider of the genus Orchestina (family Oonopidae;
Fig. 4) and a mymarommatoid wasp of the genus Galloromma (family Gallorommatidae; Fig. 4), both of which
are currently under study (e.g., Ortega-Blanco et al., in
press).
The Australian Tertiary amber is the newest project
currently underway at the ESRF. This material is found
on eastern Cape York Peninsula, and although its precise
age is the subject of current investigation, its entomological content and geological context suggest a Tertiary
age (Bickel, 2009). All the material scanned at the ESRF
involved fully opaque pieces; hence the same technique applied to the French Cretaceous opaque amber
samples was implemented. From this survey, several
arthropod and plant inclusions were recognized, including hymenopterans, hemipterans, dipterans and a diverse
group of beetles, some within the family Scolytidae
(Fig. 5).
Because of the utility of this method and its relevance for amber research, new projects on other significant
amber deposits will begin in the near future at the ESRF.
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Fig. 4. 3D reconstructions of Lower Cretaceous Spanish amber arthropods using PPC-SRCT at BM05 beamline, ESRF, Grenoble. 1: Female spider from
San Just outcrop (Orchestina, Oonopidae), specimen CPT-4100, general habitus, voxel size 0.7 m, propagation distance 100 mm, 20 keV. Scale bar 500 m.
2: Galloromma sp., specimen MCNA12630, a wasp of the mymarommatoid family Gallorommatidae from Peñacerrada I outcrop. Voxel size 0.56 m,
propagation distance 25 mm, 25 keV. Scale bar 500 m.
Fig. 4. Reconstructions 3D d’arthropodes dans l’ambre Crétacé inférieur d’Espagne, effectuées par PPC-SRCT sur la ligne de lumière BM05, ESRF, Grenoble.
1 : Araignée Oonopidae femelle (Orchestina sp.) du gisement de San Just, spécimen CPT-4100, aspect général, taille de pixel 0,7 m, distance de propagation
100 mm, 20 keV. Barre d’échelle 500 m. 2 : Galloromma sp., spécimen MCNA12630, guêpe mymarommatoïde de la famille Gallorommatidae du gisement
de Peñacerrada I. Taille de pixel 0,56 m, distance de propagation 25 mm, 25 keV. Barre d’échelle 500 m.
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Fig. 5. 3D reconstruction of a scolytid beetle (Scolytidae) from Tertiary Australian amber using PPC-SRCT at ID19 beamline, ESRF, Grenoble. Voxel size
1.37 m, propagation distance 150 mm, 30 keV. Scale bar 1 mm.
Fig. 5. Reconstruction 3D d’un Coléoptère Scolytidé dans l’ambre tertiaire d’Australie, effectuée par PPC-SRCT sur la ligne de lumière ID19, ESRF, Grenoble.
Taille de pixel 1,37 m, distance de propagation 150 mm, 30 keV. Barre d’échelle 1 mm.
All projects are closely related through what is now one
of the largest worldwide collaborations on the study of
amber.
Acknowledgements
We would like to thank Jose Baruchel, Elodie Boller, and
others of ESRF beamlines ID 19 and BM 05 for their support
and assistance over the years. This work is a contribution to the projects AMBRACE no. BLAN07-1-184190 from
the French National Research Agency, CGL2008-00550/BTE
from the Ministry of Science and Innovation of Spain,
DP0881440 from the Australian Research Council, and “The
Study of the Fossil Insects in Lebanon and their Outcrops:
Geology of the Outcrops–Historical and Biodiversity Evolution” from Lebanese University. We also thank Beth
Norris and Dale Wicks for access to opaque Australian
amber analysed in this study. We are grateful to Luis Alcalá
(Dinopolis), Jesús Alonso (Museo de Ciencias de Álava) and
Fermín Unzué (El Soplao) for providing material from the
Spanish amber outcrops.
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