MESSAGE
| DATE | 2017-03-09 |
| FROM | Ruben Safir
|
| SUBJECT | Subject: [Hangout-NYLXS] Non-Destructive scanning of TREX
|
http://www.ndt.net/article/wcndt2016/papers/fr2c4.pdf
Abstract.
In 2016, the Dutch national natural history museum, Naturalis
Biodiversity Center in Leiden, will present its Tyrannosaurus rex skeleton to the
public, the first original T. rex skeleton on permanent display outside North
America. The 66
-
million year old f
ossil was discovered in 2013 near Jordan,
Montana, USA, and excavated by PL and AS and team
in the autumn of the same
year.
The well
-
preserved and nearly complete skull made a CT scan of the fossil,
prior to preparation, mandatory. The skull measures almo
st 1.5 m in length, and the
surrounding sandstone matrix, in turn wrapped in a protective plaster jacket, made
the use of a conventional CT system not an option
–
both because of specimen
weight, as well as specimen size and thus required penetration lengt
h.
Therefore, the T. rex skull was scanned with the unique XXL
-
CT system of the
Fraunhofer Development Center X
-
ray technology (EZRT), which is capable of
handling specimens of up to 10 metric tons in weight and a few meters in diameter
(e.g. complete cars
). The X
-
ray source for this system is a pulsed 9 MeV linear
accelerator. This allows for enough penetration power in both very large and highly
absorbing specimens. The X
-
ray detector is a custom
-
made line detector array, 4 m
wide.
In this contribution we
describe the XXL
-
CT system and present the challenges,
considerations and
preliminary
results of the CT
-
scan of the 1.5 m long T. rex skull.
1.
Introduction
The 13 m long carnivorous dinosaur Tyrannosaurus rex is arguably the dinosaur best
known by the general publi
c (Brochu, 2003). With a new dinosaur gallery scheduled to
open in 2018, the national natural history museum of the Netherlands, Naturalis
Biodiversity Center, in Leiden, set out to acquire an original skeleton of this dinosaur. A
skeleton of Tyrannosaurus
rex was discovered in Spring and excavated in the Fall of 2013,
from a sandstone stream channel of the Hell Creek Formation near Jordan, Montana, USA.
The excavation relied upon a close collaboration between Black Hills Institute and
Naturalis (Schulp et
al., 2015). Reasonably complete skeletons of Tyrannosaurus are few
and far between, and so far only two skeletons
substantially
more than 50% complete have
been found (Larson & Carpenter, 2008). At the moment of submission of the present paper
(March 2016), the Naturali
s T. rex skeleton is still being prepared, and is currently
More info about this article:
http://ndt.net/?id=19249
2
scheduled to go on public display in Leiden in September 2016, where it is registered under
collection number RGM 792.000.
The specimen comprises a well
-preserved skull, partial cervical and dors
al vertebral series,
an almost
-complete rib
-cage, scapula
-coracoid, furcula, a complete pelvis, the right leg, and
about half of the tail
. Probably no other innovation has had a similarly profound impact on
the study of fossil vertebrates in the last few d
ecades than the increased accessibility and
improvement in image quality of CT scanning (e.g., Leiggi & May, 2003). The non-
destructive character of CT allows for features otherwise inaccessible, to be visualized
,
described, compared and analyzed
(Mallison
, 2011; Abel et al., 2012). Medical CT
-
scanners, with a bore suited to fit most humans, and, occasionally, veterinary CT scanners
with a larger bore, now routinely allow for scanning of human-
sized objects; however, the
specifications of th
ose
imaging systems
are optimized for objects less dense than fossils,
and the X
-ray performance is dimensioned for X
-ray exposures “as low as reasonably
achievable” (the ALARA safety principle). This is not necessarily the specification set
required for successful imaging of
higher density
objects such as large, heavily
per
mineralized fossils.
Successful scans of extremely large paleontological
objects can, therefore, be challenging.
Scanning the skull of one of the largest carnivores ever to have walked the earth is certainly
beyond the capabilities of a regular medical CT system. The skull of the remarkably
complete T. rex skeleton FMNH PR2081, perhaps better known by its nickname “Sue”
(now on display at the Field Museum in Chicago) was scanned –almost two decades ago
–
at Rocketdy
ne Division of Boeing North America. This scan was completed in a Minatron
205 scanner, yielding 748 coronal slices, 2 mm in thickness (Brochu, 2003). For many
paleontological questions however, higher
-resolution imaging than 2 mm voxel size is
necessary.
In this contribution, we elaborate on the technical challenges in scanning the
skull of the Naturalis T. rex. A more detailed description of the morphology, partially based
on the CT scan data discussed here, will be submitted for publication elsewhere.
2. M
aterials and Methods
System Setup
During the last few years the Fraunhofer Development Center X
-Ray Technology (EZRT)
focused on the research of CT imaging methods in the high energy regime to overcome the
otherwise quite narrow scope and limitation
s of conventional X
-ray systems regarding
specimen s
ize and material composition. This finally resulted in the development of a CT
system capable of scanning very large objects of up to 5 m in at least one axis. The so
called XXL
-CT system was installed in Fürth, Germany in 2013 (Fuchs, 2016). To our
knowle
dge, the XXL
-CT is the first and l
argest
publicly available CT system for the
inspection of such objects. The XXL
-CT features some unique characteristics when
compared to conventional CT systems. Imaging of objects like complete cars or shipping
containers
require penetration lengths of more than 200 mm of steel or equivalent. To
achieve enough penetration power, the system r
elies upon
a linear accelerator (linac) with
up to 9 MeV X
-ray energy and a dose rate of up to 25 Gy/min at 1 m distance. Figure 1
shows
the X
-ray bremsstrahlung spectra for 6 and 9 MeV with 10 cm of Aluminum as
prefilter. The data was acquired with Monte
-Carlo simulation toolkit ROSI (Giersch 2003).
Both spectra look fairly similar with a mean energy of 1.8 and 2.5 MeV respectively.
3
Fig. 1.
Linac bremsstrahlung spectra for 6 and 9 MeV electrons.
When choosing the appropriate detection system
, the still significantly higher X
-ray
energies compared to conventional systems have to be taken into account. At present, flat
panel detectors are no
t a practical option when
scan
ing
large objects efficiently
, due to both
technological limitations and the X
-ray attenuation characteristics. The dominant
attenuation effect in the MeV range is Compton scattering (compare Berger 1998). Here a
line detector pro
vides a significantly better image quality which is mainly due to the non-
detection of scattering in the plane orthogonal to the sensor. Certainly the
most significant
trade-
off is an increase in scanning time. Another effect arising from Compton scattering is
that the ima
ging properties are mainly determined by
the density of the penetrated material
and only to a small amount by
the atomic number. This results in a better linearity for
multi-
material specimen
s as well as a better detectability of low
-Z and high
-Z elements.
We
chose a line detector array of about 4 meters in length and a pixel pitch of 0.4 mm. This
results in nearly 10,000 pixels. A 10 mm thick scintillator of cadmium tungstate provides a
reasonable quantum efficiency of 45% for a 9 MeV bremsstrahlung spectrum. Both the
linac and the horizontally orientated detector are mounted on two towers of 8 m height (see
figure 2). A three
-meter diameter turntable is placed in front of the detector tower. The
system allows for reconstruction volumes of 3.2 m (and more wi
th limited angular range) in
diameter and 5 m in height. The maximum specimen weight is 10,000 kg.
Fig.
2.
Mechanical setup of the XXL
-CT system
.
The CT scanning process with this system is done in a fan beam geometry. The source and
detector are movin
g synchronously upwards during image acquisition. To compute a 3D
-
representation of the specimen a multitude of projections are acquired each from a different
4
viewing angle. This is achieved by rotating the turntable between each subsequent image by
one sm
all angular step.
Composition of the fossil
Excavating and removing large fossils from the field is generally done using a technique
called ‘plaster jacketing’ (e.g., Leiggi &
May, 2005). Briefly summarized, a fossil is
exposed by removing the surrounding
matrix, and the exposed bones are impregnated with
a consolidant. Subsequently, a trench is dug around the fossil, essentially leaving the fossil
exposed on a ‘pedestal’. The bone surface
is covered in aluminum foil or wet tissues to act
as a barrier to the plaster jacket, which is subsequently applied. This plaster jacket is
essentially a composite material, consisting of burlap and plaster of Paris. In larger blocks
(such as the T. rex s
kull block) the jacket is reinforced with a wooden support structure,
which also acts to provide grip and leverage in handling the block. The resulting plaster
jacket, then, has become a composite of a wide variety of materials with a wide variety of
X-ray
absorbing properties: fossil bone, fossil tooth enamel, surrounding sandstone, the
occasional
concretionary growth
of the mineral pyrite (FeS2; clearly visible in the scan),
plaster, burlap, wood and metal screws to hold the wooden frame together. Figure 3 shows
a photograph of the skull
, within its overturned plaster jacket,
being prepared at the
excavation site.
Fig. 3.
Preparation of the skull at the excavation site.
Preparation of the skull for scanning
The CT scan geometry of the XXL
-CT setup made it desirable to place the skull in an
upright orienta
tion, i.e. the skull on the turntable is rotated around its longitudinal axis. This
yields two advantages over the natural orientation. First the maximum X
-ray penetration
length through the skull and surrounding sandstone matrix is significantly reduced (
factor
of 2) and more homogeneous over the 360° range (see figure 4) and second the smaller
cross
-section reduces blurring effects due to X
-rays impinging the detector at an angle
(signal spread over more than one pixel). Both effects highly influence the image quality
both in terms of contrast as well as spatial resolution.
5
Fig. 4.
Top view of crate with skull included when scanning in natural orientation (left) and upright
orientation (right). The arrow marks the estimated maximum penetration length for
both setups.
This provided an additional challenge in preparing the specimen for transport and scanning,
as the way the fossil was crated had to ensure that the specimen was sufficiently tightly
packed to allow for tipping 90° in the first place, while a
t the same time guarantee
sufficient cushioning as to have the fossil survive transport (road and air transport, where
turbulence cannot be ruled out), and on the other hand guaranteeing that the specimen did
not move at all in the crate while scanning. This was achieved by first completing the
plaster jacket so that the fossil was completely enclosed and the surface of the skull
protected from movement within the jacket. Secondly the jacket had to be immobilized
within the wooden crate. This was accomplished by adding more wooden supports to the
plaster jacket and then screwing additional wooden supports between the jacket and the
crate. To completely eliminate the possibility of movement, the remaining air space within
the crate was then filled with 2# density polyur
etha
ne foam.
CT-Scan parameters
The skull, at the time of scanning, was still encased in the sandstone matrix
and the plaster
jacket and immobilized within the
wooden crate. The crate containing the T.
rex skull
weighed in at about 700 kg. For scanning t
he crate was put in an upri
ght orientation and
hoisted onto
the turntable with a ceiling crane. The CT scan was performed with the
acquisition parameters summarized in table 1. Taking into account the system
magnification of 1.2, the effective pixel size was 0.33 mm; however the CT re
construction
was performed at lower resolution with a binned voxel size of 1 mm to significantly
improve the signal
-to-noise ratio.
Tab.1.
Acquisition parameters for the CT scan.
X
-
ray energy
9 MeV
Scanning time
~48 h
Angles
1500
Pixel size
0.4
mm
Vertical sampling
0.5 mm
Voxel size
1 x 1 x 1 mm³
6
3. R
esults
The CT reconstruction was performed on the whole dataset including the surrounding crate
and support structure. Figure 5 shows one slice through the dataset. Generally, the bones
(light grey)
can be clearly distinguished from the sandstone matrix (dark grey)
due to its
significant difference in density
. Inside the bone, one can discern occasional high-
intensity
spots which represent pyrite concretions. Other materials involved in packing and cr
ating
have generally much lower X
-ray absorption, except for the screws used in the wooden
support frame. As can be seen in the upright corner of figure 5 even the polyurethane foam
is visible by using a different grey value scaling.
Fig. 5.
CT slice
through the skull. The skull bones clearly stand out from the sandstone matrix and
the supporting structures.
Figure 6 (left) shows a 3D
-rendering of the same dataset. To distinguish the different
materials a false-
color representation based on the diffe
rent absorption values of the
materials were used. The virtually removed sideways uncovers the wrapping around the
skull and sandstone block as well as the additional wooden supporting structures. Figure 6
(right) cuts through the crate in lateral directio
n and shows the interior
of the skull and
sandstone block. The white colored structure marks the bone fragments.
The next step was to virtually excavate the skull. The good material contrast made it
possible to mask out the bulk of the sandstone matrix and the supporting structures by
setting appropriate thresholds. High absorption parts like the screws as well as noise
particles had to be removed manually. The result of this segmentation can be seen in figure
7. At this stage the segmented skull is still re
presented by three dimensional pixels (Voxels)
with a specific
absorption value. To allow for further
processing in CAD software e.g. for
3D
-printing
preparation
the segmented skull was converted to a triangular surface mesh in
the stl Format.
7
Fig.
6.
3D
-rendering
of the CT dataset with crate sideways
removed (left). Cutting through the crate
in lateral directions reveals the bone structures inside the sandstone matrix (right).
Fig.
7.
Virtual excavation of the skull by removing the sandstone matrix and support structures
.
4. D
iscussion and Outlook
The scan has already allowed for much more efficient preparation work on the fossil, by
showing which areas deserve particular attention. Many internal features are clearly visible,
including pneumatic cham
bers and the portion of the skull that was originally occupied by
the brain (Witmer & Ridgely, 2009). Of particular interest are the morphology of the nerve
channels, semicircular canals of the inner ear (Witmer & Ridgely, 2009), location and form
of the s
tapes, the possibility of respiratory turbinates (Witmer, 1997; Brochu, 2003; Witmer
& Ridgely, 2009), and the fact that this scan shows new fragile structures not visible with
lower resolution CT scans –
and which we suspect may have been obliterated by
mechanical preparation of other specimens. We do hope that this scan, too, will contribute
to a more informed reconstruction of soft tissues (Witmer, 1997; Brochu, 2003).
Part of the magic of X
-ray imaging techniques is that the invisible becomes visible. The CT
of the T. rex skull allowed for a virtual endocast of the brain cavity to be made (compare
Witmer & Ridgely, 2009). A 3D
-print of the “brain” of the T. rex (
see
Figure 8) already
played a role in lectures and (online) classes; the printed brain will
also find a place in the
upcoming exhibition at Naturalis
.
8
The skull of the new T. rex shows multiple pathologies, some of which are captured in
detail in the CT scan. Pathologies include a rather large bone infection which has removed
bone tissue in the anterior part
of the right maxilla (=the front end of the upper jaw); this
element however was discovered separate from the main skull block, and therefore was not
part of the scan. The same applies for the posterior mandibular unit (= the rear part of the
lower jaw), which is graced by a series of healed puncture wounds; considering the size and
spacing of the wounds, in all likelihood this individual was bitten by another T. rex -
and
lived
for the wounds to heal
. Other pathologies on the skull include scratch marks on the
left side
of the skull.
At Naturalis
we plan
to present the CT data of the skull in an
interactive display, where a laser line projected on a scaled, moveable 3D
-print of the skull
acts as a pointer to the CT
-imagery shown beside the skull. Interactive “hot zones” allow to
conne
ct explanatory text and video to the features highlighted in the scan.
Fig.
8.
Extraction of the brain segment (blue) for further processing to a
3D
-printer
.
5. Acknowledgements
Many thanks to TNT Special Services in The Netherlands, for generously offering to ship
the precious cargo from the lab in the US to the scanner in Germany, and then back again
for further preparation. Robert van Liere of the Centrum voor Wiskunde en Informatica,
Universiteit van Amsterdam extracted the brain virtual endocast
, and Ultimaker kindly
provided support in 3D
-printing.
6. References
Abel, R. L., Laurini, C. R., & Richter, M. (2012). A palaeobiologist's guide to ‘virtual’
micro
-CT preparati
on. Palaeontologia Electronica.
Berger M.J., Hubbell J.H., Seltzer S.M., Coursey J.S., and Zucker D.S. (1998) XCOM:
Photon Cross Sections Database, NIST Standard Reference Database 8.
9
Brochu, C.A. (2003) Osteology of Tyrannosaurus rex: Insights from a nearly complete
Skeleton and High-
Resolution Computed Tomographic Analysis of the Skull. Journal of
Vertebrate Paleontology, 22:sup4, 1-
138, DOI: 10.1080/02724634.2003.10010947
Fuchs, T. et al. (2016). High-
energy 3D X
-ray computed tomography on very large
objects," to be published .
Giersch, J. et al. (2003) ROSI
an object
-orie
nted and parallel
-computing monte carlo
simulation for X
-ray imaging. Nuclear Instruments and Methods in Physics Research 509.
Larson, P. & K. Carpenter (Eds.), 2008. Tyrannosaurus rex: The Tyrant King. Indiana
University Press, Bloomington, Indiana, 435 pp.
Leiggi, P. & P. May (Eds.), 2005. Vertebrate paleontological techniques, Vol. 1.
Cambridge University Press, New York., 366 pp.
Mallison, H. (2011). Digitizing Methods for Paleontology: Applications, Benefits and
Limitations.
In Computational Paleont
ology (pp. 7
–43). Berlin, Heidelberg: Springer Berlin
Heidelberg. http://doi.org/10.1007/978-
3- 642-
16271-
8_2
Schulp, A.S., D. Bastiaans, P. Kaskes, P. Manning & P. Larson (2015): A New, Mature and
Pathologic specimen of Tyrannosaurus rex. Society of Verte
brate Paleontology Annual
Meeting, Dallas.
Witmer, L.M. (1997). The evolution of the antorbital cavity of archosaurs: a study in soft
-
tissue reconstruction in the fossil record with an analysis of the function of pneumaticity.
Society of Vertebrate Paleon
tology Memoir 3: 75 pp.
Witmer, L. M., & R. C. Ridgely (2009). New Insights Into the Brain, Braincase, and Ear
Region of Tyrannosaurs (Dinosauria, Theropoda), with Implications for Sensory
Organization and Behavior. The Anatomical Record: Advances in
Integrative Anatomy and
Evolutionary Biology, 292(9), 1266–1296. http://doi.org/10.
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