University of Nevada, Reno
Three-dimensional visualization of the Berlin-Ichthyosaur State Park fossil beds from terrestrial LiDAR data
A thesis submitted in partial fulfillment of the requirements for the degree of
Bachelor of Science in Geology and the Honors Program
by
Paige dePolo
Dr. Paula Noble, Thesis Advisor
Dr. Robert Watters, Thesis Supervisor
May, 2016
UNIVERSITY OF NEVADA THE HONORS PROGRAM RENO
We recommend that the thesis prepared under our supervision by
Paige dePolo
entitled
Three-dimensional visualization of the Berlin-Ichthyosaur State Park fossil beds from terrestrial LiDAR data
be accepted in partial fulfillment of the requirements for the degree of
BACHELOR OF SCIENCE, GEOLOGY
______Paula Noble, Ph.D., Thesis Advisor
______Robert Watters, Ph.D., Thesis Supervisor
______Tamara Valentine, Ph. D., Director, Honors Program
May, 2016 i
Abstract
A terrestrial LiDAR (Light Detection and Ranging) unit was used to scan an in situ death assemblage of the enormous Late Triassic ichthyosaur, Shonisaurus popularis, with the goal of testing the applicability of this method in creating three-dimensional digital models of large fossil sites. The fossil beds are located at Berlin-Ichthyosaur State Park in
Nye County, Nevada where they are protected by a permanent shelter, the Fossil Hut.
Thirteen scan locations were used to survey both the exterior and interior of the Fossil
Hut. The point cloud of the quarry model was composed from nine high-resolution scans.
Digital measurements of the length of selected skeletal elements in the quarry model correspond well to caliper measurements of the same elements in the field. The millimeter scale resolution of the S. popularis remains demonstrated by the LiDAR point cloud is suitable for analysis of gross bone structures and represents a viable means of digitally capturing in situ fossil sites. The LiDAR model allows for the accurate measurement of the spatial relationships between skeletal elements and provides an important baseline for conserving in situ fossil exhibits.
ii
Acknowledgements
I would like to express deepest appreciation to my thesis advisor, Dr. Paula Noble, who was willing to invest a great deal of time and effort outside of her field of specialization to support my ‘vertebrate tendencies.’ With Paula on sabbatical this year, I am also deeply grateful to Dr. Bob Watters for stepping into the role of on-campus resource and project supervisor.
Much thanks is also due to the team from the Smithsonian Institution’s National
Museum of Natural History and Digitization Program Office: Dr. Neil Kelley, Dr. Nick
Pyenson, Holly Little, and Jon Blundell. Neil (the PI of this investigation) has been an excellent resource - not just on ichthyosaurs – but for a young scientist learning how to be an effective collaborator on a larger project. The project has grown from its initial inception and new folks have joined the team. Dr. Randy Irmis and his PhD. student,
Conny Rasmussen, are wonderful additions to the team and their field perspective on a project that was spiraling into virtual reality has helped to keep the whole crew grounded.
Material support for this project came from a variety of University of Nevada, Reno sources. The Center for Neotectonic Studies (Steve Wesnousky and Steve Angster) allowed me to borrow a terrestrial LiDAR machine and to use their licensed software to process the data. Speaking of licenses, Gabe Plank (Nevada Seismological Laboratory) is a computer ninja has been a huge help in renewing and updating the license files. The staff at the DLM library (Dr. Tod Colgrove, Chrissy Klenke, Tara Radiecki, Sierra
Gonzales, and Dwight Boyko) has also been generous with their time and library resources. Despite the great danger presented to fancy equipment by dust, the DLM library staff allowed me to check out scanners and laptops and bring them to the field. iii
This library does indeed rock! Dr. Jim Carr generously let me borrow his portable generator in order to power this equipment. Thank you for bringing light to the desert!
Thanks is also due to Russ Fields, Director of the Mackay School of Earth Sciences and
Engineering for provided dedicated funds to support a trip to the Smithsonian Museum of
Natural History to use better computers. This research was also facilitated by a General
Undergraduate Research Award (GURA) from the Office of Undergraduate Research.
Finally, thank you to my fellow students, Taylor Krabiel and Riley Kellermeyer, for being willing to give up a weekend and to be my wheels and field assistants.
To Dr. Tamara Valentine, Director of the Honors Program, I owe much of my sanity.
Thank you for working with my unique research schedule and for letting me make my own path as an Honors student.
Finally, great thanks is due to my parents, Craig and Diane, who have been incredibly supportive of my first foray into the professional world of science. I’ll never forget the mad vehicle shuffle after our first round of field work where the pair of you dropped everything to make sure the Smithsonian folks and their equipment all got to the plane on time.
Dedication
This work is dedicated to Robin Riggs (February 1, 1960-October 18, 2014). His years of service as a park ranger at Berlin-Ichthyosaur State Park touched many lives. Robin, your insight and enthusiasm are missed.
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Table of Contents Abstract i Acknowledgements ii Dedication iii Table of Contents iv List of Tables v List of Figures vi List of Visualizations vii Introduction 1 Background Site Characterization and History 2 Description of Shonisaurus popularis 5 Theories for Death Assemblage at BISP 6 Terrestrial LiDAR 8 Methods Data Collection 8 Data Processing 10 Results 11 Discussion Orientation of Skeletal Elements in Relation to Death and Taphonomy 16 Exhibit Monitoring and Fossil Preservation 18 Conclusion 19 References 21 Appendix I: Stratigraphic Column of Geologic Units in Berlin-Ichthyosaur State Park 24 Appendix II:Pylogenetic Tree of Ichthyosaurs 25 Appendix III: Schematic of Terrestrial LiDAR Scanner Locations Relative to Major Features of Fossil Hut 26 Appendix IV: Comparison of Field Measurements with Scan Measurements 27
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List of Tables
Table 1: Field Observations vs. Point Cloud Measurements 27
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List of Figures
Figure 1: Location of Berlin-Ichthyosaur State Park in Nevada 3 Figure 2: Locations of Camp’s Quarries 3 Figure 3: Geologic Map of Berlin-Ichthyosaur State Park 4 Figure 4: Camp’s Skeletal Reconstruction of Shonisaurus popularis 5 Figure 5: Kosch’s Skeletal Reconstruction of Shonisaurus popularis 6 Figure 6:”U” Vertebrae of the Visitor’s Quarry 7 Figure 7: Complete Terrestrial LiDAR Scanner Setup 9 Figure 8: Scan Coverage in Quarry 10 Figure 9: LiDAR Quarry Model 12 Figure 10: Distance Measurements in Point Cloud 13 Figure 11: Comparison of Field and Point Cloud Measurements 14 Figure 12: Taylor Diagram Comparing LiDAR Model with Field Observations 15 Figure 13: Coracoid-Vertebrae Relationship 16 Figure 14: Skeleton Orientation Interpretation of Visitor’s Quarry 17 Figure 15: Concrete Retaining Wall in Quarry 18 Figure 16: Stratigraphic Column of Geologic Units in Berlin Ichthyosaur State Park 24 Figure 17: Phylogenetic Tree of Supraorder Ichthyopterygia 25 Figure 18: Scanner Locations Schematic 26
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List of Visualizations
Visualization 1: Overview of Fossil Hut 9 Visualization 2: Flyover of Visitor’s Quarry 11 Visualization 3: Specimen I Vertebral Column and Coracoids 17
The files for all visualizations are located on the supplemental disc for this manuscript. 1
I. Introduction
Since its systematization as a science, vertebrate paleontology has faced the problem of fossil access. Namely, if a set of bones is curated at a museum, then the only individuals able to work on the bones are those who are both knowledgeable and who have physical access to the museum. Three-dimensional technology provides a solution to this problem of fossil access through the generation of multiple clear three-dimensional images of the bones in question that can then be disseminated to multiple individuals for study from afar (Cunningham et al., 2014). Three-dimensional imaging also allows for a better analysis of how ancient organisms looked and moved by facilitating the visualization, manipulation, and rotation of their skeletal elements. Additionally, the potential for non-destructive analysis of the bones opens up new pathways of inquiry for paleontologists interested in the nature of soft tissue in prehistoric animals (Cunningham et al., 2014).
The power of three-dimensional data also speaks strongly to the puzzle of effective conservation of large fossils that are left permanently in situ, embedded in the rock.
Several of these sites exist in the United States including Dinosaur National Monument
(Utah), the Mammoth Site (Hot Springs, South Dakota), Ashfall Fossil Beds State
Historical Park (Nebraska), and, the study area of this thesis, Berlin-Ichthyosaur State
Park (Nevada). Three-dimensional images provide the potential for electronic curation of fossils and monitoring the deterioration that cannot be removed from the location where they are found. Data from such studies can be used to propose preservation plans for fossil resources. These plans, which include shoring up unstable support structures, aid in allowing the fossils to survive for future viewing and study. 2
Many different methods of capturing three-dimensional images of fossils - including
photogrammetry, computerized tomography (CT), and magnetic resonance imaging
(MRI)- have been employed to visualize vertebrate fossils (Cunningham et. al., 2014;
Pyenson et al., 2014). One three-dimensional visualization technique, terrestrial LiDAR
(Light Detection and Ranging), has been previously applied to dinosaur trackways to
produce a digital model of the sites (Bates et al., 2008; Bates et al., 2009). However,
terrestrial LiDAR has not been previously used to describe in situ vertebrate fossils.
Terrestrial LiDAR provides advantages over other three-dimensional techniques with its
portability and short field collection time.
The immediate goal of this study is to evaluate the feasibility of using terrestrial
LiDAR as a way to three-dimensionally image such in situ vertebrate fossil sites. The
case area for this study is the Visitor’s Quarry in the Fossil Hut at Berlin-Ichthyosaur
State Park (Nye Co., Nevada). This iconic site contains at least nine adult individuals of
Shonisaurus popularis, Nevada’s state fossil. A secondary goal of this study is to
determine whether the images captured terrestrial LiDAR can be used to make
interpretations about the mechanisms which caused so many adult individuals to be
entombed in the quarry at Berlin-Ichthyosaur State Park (BISP).
II. Background
a. Site Characterization and History
Ichthyosaurs were first observed in the state of Nevada by Leidy (Leidy, 1868). In
1929, Siemon W. Muller found ichthyosaur remains in both Union Canyon (the current
location of BISP) and in the nearby Pilot Mountains (Camp, 1980). The primary
investigations around Union Canyon were initiated after Margaret Wheat (a resident of 3
Fallon, NV) observed ichthyosaur bones weathering out of the limestone of Union
Canyon (Camp, 1980). These excavations were conducted between 1954 and 1957 by Dr.
Charles Camp (University of California Museum of Paleontology) and selected specimens were later prepared at Washoe Pines, near Carson City, Nevada (Camp, 1980).
After the establishment of the Nevada state park in 1957, active excavations of the ichthyosaurs were halted (Camp, 1980).
Berlin-Ichthyosaur State Park is located in the Union district, one of the oldest mining districts in the state of Nevada (Silberling, 1959). The park sits in the western foothills of the Shoshone Mountains above Ione Valley in Nye County, Nevada (Silberling, 1959).
Figure 1 shows the location of BISP in the state of Nevada. Figure 2 shows the location
Figure 1: Location of Berlin-Ichthyosaur Figure 2: Locations of Camp’s Quarries. Sketch map of the State Park in Nevada. The yellow star location of Berlin-Ichthyosaur State Park in the state of Nevada denotes the park in northern Nye County. with details of individual quarry locations (Camp, 1980). of the fossil quarries that Charles Camp discovered in West Union Canyon (Camp 1980).
Quarries 2 and 3 in Figure 2 were eventually combined into the Visitor Quarry in the 4
Fossil Hut. This area was mapped and the stratigraphy was described in detail by
Silberling (1959).
Ichthyosaur fossils (Shonisaurus popularis) are found in the shaly limestone member of the Luning Formation immediately below the Carnian-Norian boundary of the Late
Triassic (Camp, 1980). The Carnian-Norian Boundary is approximately 227 million years old (Cohen, Finney, and Gibbard, 2014). Figure 3 shows a geologic map of Berlin
Ichthyosaur State Park. This map details the subdivisions of the Triassic Luning
Formation (particularly the shaly limestone member where ichthyosaur fossils are found).
The Visitor’s Quarry in the Fossil Hut is denoted in Figure 3 using a red star.
Figure 3: Geologic Map of Berlin-Ichthyosaur State Park. This map shows the extent of the shaly limestone member of the Luning formation (Trll) – the unit where ichthyosaur fossils have been observed. The red start denotes the location of the Visitor's Quarry (modified from Balini, 2014).
The ichthyosaurs can be stratigraphically constrained using the ammonite stratigraphy delineated by Silberling (1959). The majority of the ichthyosaur bones have been 5
observed in Silberling’s Klamathites macrolobatus zone with isolated pieces also
observed in Silberling’s Klamathites schucherti zone and the Juvavites elegans zone
(Camp, 1980). Appendix I contains a stratigraphic column showing the relationship
between the members of the Luning formation, Silberling’s ammonite stratigraphy, and
the divisions of the geologic time scale. b. Description of Shonisaurus popularis
Shonisaurus popularis is Nevada’s state fossil. Nevada designed S. popularis its state
fossil in 1977 (NRS 235.080).
These organisms were roughly 14-15 m in length (Camp, 1980). Figure 4 depicts the
original skeletal reconstruction of S. popularis proposed by Charles Camp in 1980.
Figure 4: Camp’s Skeletal Reconstruction of Shonisaurus popularis. The original skeletal reconstruction was proposed in 1980. The large size of the head relative to the body and the distribution of the rib bones are particularly notable because they were later revised based on evidence in the Visitor's Quarry. The black line underneath the tail is 1 m scale bar.
Kosch (1990) proposed the following skeletal revisions for S. popularis after examining
the display specimens at the Berlin-Ichthyosaur State Park fossil quarry: the reduction in
the size of the head, paddles, and tail and the elongation of the body. These changes
caused the overall shape of the ichthyosaur to become more streamlined. These changes
resulted in an organism more consonant with the forms of other late Triassic
ichthyosaurs. Kosch’s revision provides the frame of reference for whole-body 6
interpretations of the quarry specimens in context of this thesis. Figure 5 depicts a lateral
view of the revised skeletal reconstruction of S. popularis.
Figure 5: Kosch's revised skeletal reconstruction of Shonisaurus popularis (1990). The black line below the ribs is a scale bar that denotes one meter. The genus Shonisaurus belongs to the infraorder Shastasauridae (McGowan and
Motani, 2003). Shonisaurus popularis is one of the largest species of ichthyosaurs ever to
exist (McGowan and Motani, 1999). Appendix II shows a phylogenetic tree of the
supraorder Ichthyopterygia (to which Shonisaurus belongs (Motani, 1999). Although
Camp originally recognized three species of Shonisaurus (S. popularis, S. mulleri, and S.
silberlingi) in his 1980 paper, later revisions have declared S. mulleri and S. siberlingi as
nomen dubiae (McGowan and Motani, 1999). All individuals in the Visitor’s Quarry are
interpreted to be representatives of S. popularis (Camp, 1980). c. Theories for Death Assemblage at BISP
The presence of at least seven adult ichthyosaur skeletons in a small space (the
Visitor’s Quarry is ~15 m x 25 m) begs the question – what killed these animals? Several
hypothesis have been posited in response to this question. Charles Camp, the original
excavator of the Visitor’s Quarry at BISP, suggested that the ichthyosaurs were beached
due to the subparallel alignment and the degree of articulation of the skeletons (1980).
However, this theory proves untenable because the ichthyosaurs are found in the upper
section of the Luning Formation – a fine-grained shaly limestone member that bears the 7 sedimentological characteristics of a deeper water environment. The rock type observed is inconsistent with beach deposits and instead indicates a shallow shelf environment of deposition. Therefore, alternatives to Camp’s original hypothesis have been advanced in subsequent work. One such alternative is phytotoxin poisoning via the ingestion of the metabolic biproducts of planktonic species like dinoflagellates and diatoms (Hogler,
1992). The scenario described can be conceptualized using the modern analogue of a red tide (algal bloom). Hogler suggests that this mechanism explains why mass mortality has been observed only for S. popularis (1992). As organisms occupy successively higher tropic levels in their environment, the toxins from planktonic species become more and more concentrated.
These concentrations reach fatal levels in top predators like ichthyosaurs (Hogler 1992). The most colorful alternative theory posited thus far suggests that the death assemblage of the Visitor’s
Quarry at BISP is a giant kraken midden
(McMenamin, 2011). This theory hinges on the observation that some of the vertebrae in the
Figure 6: "U" vertebrae of the Visitor's Visitor’s Quarry exhibit an imbricated pattern Quarry. These bones show a distinctive pattern of imbrication. McMenamin argues (Figure 6) that could be indicative of “the sucker that this pattern is indicative of a self- portrait of a large cephalopod that preyed upon the ichthyosaurs (2011). arrays on cephalopod tentacles” (McMenamin, p.
55, 2011). While this theory has captured the imagination of the general public, no evidence supporting the presence of such a cephalopod has been observed at BISP to 8
date. In summary, although multiple theories have been proposed to explain the death
assemblage at the Visitor’s Quarry, none have presented satisfactory geological evidence
for their respective mechanisms and the cause for this large concentration of individuals
is still open to debate.
d. Terrestrial LiDAR
LiDAR (Light Detection and Ranging) measures return interval of laser impulses (how
long it takes for a laser beam to reach an object, bounce off the object, and return to the
sensor) (Glennie, 2007). Knowledge of the precise location of the scanner allows for the
determination of the location of the object measured in three-dimensional space (Glennie,
2007). Terrestrial LiDAR has been practical applications in a variety of fields – including
forestry, landslide management, and geomorphology (Hopkinson et al., 2004; Jaboyedoff
et al., 2012; Brodu and Lague, 2012). Despite its extensive use in other fields, terrestrial
LiDAR has had very limited use in paleontology. Terrestrial LiDAR has been used to
describe and quantify dinosaur trackways in several instances (Bates et al., 2008; Bates et
al., 2009). However, this technique has not previously been employed in describing in
situ vertebrate fossils.
III. Methods
a. Data Collection
The LiDAR data were collected in and around the “Fossil Hut” at Berlin-Ichthyosaur
State Park. A Maptek 8800 LiDAR unit was used to collect georeferenced point data.
After the LiDAR unit was set up and leveled on a tripod, the range over which the
scanner would collect data was specified on an external touch-screen controller. Figure 7
shows the terrestrial LiDAR scanner set-up used to collect the point cloud data. 9
Figure 7: Complete Terrestrial LiDAR Scanner Setup. The scanner set-up consists of a leveled tripod, the scanner itself, and an external touch-screen controller. Steve Angster is inputting the desired scan coverage on the touchscreen. Photo credit: Steve Alvin.
Depending on range of the scan, the LiDAR unit took 15-30 minutes to complete each scan and collect a point cloud. The point data consist of Cartesian coordinates with associated red-green-blue color intensities.
Thirteen separate survey sites were established to provide complete coverage of the
Fossil Hut and the quarry. Appendix III contains a schematic showing the position of each scanner location relative to the Fossil Hut and the exterior mural. Four survey sites were located outside of the hut. The point cloud captured by scans from these sites is shown in Visualization 1 on the accompanying disc. Accurate GPS locations for these sites were determined using a Trimble unit. In addition to these sites, three stationary monuments (points of reference of multiple scans) were defined and surveyed. The interior of the fossil hut was surveyed from nine sites. Two of these locations were sited 10
using georeferenced monuments from the exterior of the building. The fossil quarry was
surveyed using high-resolution (1 mm point spacing) scans. Figure 8 shows the portion of
the fossil quarry captured by each scan.
Figure 8: Scan Coverage in Quarry. Each colored dotted line overlain over the line-sketch of the Visitor's Quarry denotes the area observed in an individual LiDAR scan. Low-resolution, 360° scans were also taken to encompass the interior of the fossil hut.
These scans proved particularly important for preserving accurate georeferencing because
the GPS unit was disrupted inside of the Fossil Hut and accurate location data was not
collected for scans taken within the building. b. Data Processing
The LiDAR point clouds were processed in the proprietary program, Maptek iSite Studio
5.0. Extraneous points (e.g. stray points capturing data beyond the scan object) in each
scan were identified and deleted. The scans were then manually registered. The manual
registration was necessary due to the poor georeferencing of the scans within the Fossil
Hut. Scan 3 (the scan taken closest to the exterior door) was used as the internal frame of 11 reference from which all other scans were registered. The manual registration was accomplished by manipulating the x, y, and z coordinates of the survey site and by adjusting the angle to the scanner to the measured monuments (in short, changing the location of the scanner in the virtual space). Once the scans were visually aligned, automatic registration was run to match individual point patterns across the scans. This process was performed iteratively until the quarry scans were completely referenced to one another.
IV. Results
A flyover of the final digital model is shown in Visualization 2 on the accompanying disc.
The final digital model overcame several challenges during the data processing stage.
One such challenge was the presence of smearing within the point cloud. This effect occurs when the scanner object is not positioned normal to the ray path of the laser beams. Essentially, spacing of the laser beams, while completely adequate for a continuous surface, does not provide a fine enough resolution to complete capture the edges of the object. The edge effect of smearing was overcome by cropping the scans so that only normal or near-to-normal sections of them were used for registration purposes.
While an initial goal of the data processing was to fit a smooth surface to the point cloud, this action was ultimately decided against for two reasons: a) the necessary measurements could be taken directly from the point cloud without the worries about errors that arise from interpolated surfaces and b) the necessary functions in Maptek iSite
Studio 5.0 for despiking an interpolated image were not enabled in the version of the program available for data processing. 12
After registration, the individual scans of the quarry were combined to create a single quarry model. Figure 9 shows the final result of the composited LiDAR scans. Even at the low resolution necessary to show the whole of the quarry, major features like the fault in the right-central portion of the quarry are clearly visible in the image. Qualitatively speaking, the terrestrial LiDAR model corresponded well with the physical reality of the quarry.
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2
Figure 9: LiDAR Quarry Model. This image results from the composition of all the quarry scans. Quarry-scale features like faults (shown in red) are reproduced well in the composite model. Two holes (areas of insufficient point coverage) exist in the model and are shown in yellow.
The LiDAR model performed well enough for quantitative analysis in all but two portions. The first portion (labeled 1 in Figure 9) lacked sufficient point density to reconstruct clear edges on the fossils. Figure 8 shows that this area was only covered on the outermost (least clear) portion of Scans 3 and 7. It is likely that an additional targeted scan from another location would provide the necessary data to close this hole in the model. The second place where the model failed is labeled 2 in Figure 9. This part was the lowest section of the main quarry and was shielded by the rock wall on multiple sides. 13
It is unlikely that a good scanner location could be found to correct this hole in the model.
The potential integration of other imaging techniques with the LiDAR model to fill such holes is touched upon in the Discussions section.
The quantitative
correspondence of the
LiDAR model with the
physical quarry can be
understood by
comparing field
measurements (made
Figure 10: Distance Measurements in the Point Cloud. The red line indicates the with calipers and tape distance measured across fossil B (a coracoid). As in demonstrated in this screen- capture, the point cloud is dense enough to represent subtle features in the bones accurately enough that caliper measurements can be replicated. measures) of selected bones with virtual measurements of those same bones in the point cloud. Figure 10 shows an example of how the measurements were made digitally in the point cloud. Table 1, contained in Appendix IV, shows the individual caliper measurements compared to the measurements taken in the LiDAR model. The results of this comparison strongly support the conclusion that the LiDAR scans sufficiently represent the physical reality of the quarry on the scale of tens of millimeters. 14
Four distinct skeletal elements were measured: coracoids, humeri, vertebrae, and mandibles. The femur of the most complete skeleton was also measured (Specimen I as labeled in Figure 14). Figure 11 shows the strong correspondence between the field measurements and the point cloud measurements. Each pair of bars in Figure 11 represents the measurements made upon one particular element.
250 Field Measurements Point Cloud Measurements
200
150
100 Distance Measured(cm)
50
0
(I)
(V)
L Femur (I) Femur L
Centrum (I) Centrum
Centrum (II) Centrum
Humerus
Coracoid (V) Coracoid
Centrum (IV) Centrum
Centrum (III) Centrum
Coracoid (IV) Coracoid
Mandible (IV) Mandible
L. Coracoid (I) Coracoid L.
R. Coracoid (I) Coracoid R.
L. Humerus (I) Humerus L.
R. Humerus (I) Humerus R.
R. Mandible R.
L. Coracoid (III) Coracoid L.
R. Coracoid (III) Coracoid R.
L. Humerus (IV) Humerus L.
L. Humerus (III) Humerus L.
R. Humerus (IV) Humerus R.
R. Humerus (III) Humerus R.
Figure 11: Comparison of Field and Point Cloud Measurements. This bar graph shows the correspondence between the field measurements and the measurements made in the LiDAR point cloud. The correspondence is strong with the largest discrepancy between the two measurements being ~4 cm. The point cloud measurements did not systematically under-estimate or over-estimate the field measurements and are thus a good test of the accuracy of the field measurements made by hand using calipers and a tape measure. Thus, the average percent error for all skeletal elements was 0.23%. When the percent error of particular element groups was 15 calculated, trends in over-measuring and under-measuring particular types of elements arose. The point cloud measurements for the coracoids were systematically higher than the field measurements (resulting 2.6% error) while those for the vertebrae were systematically lower (-1.9% error). The humeri measurements did not systematically overestimate or underestimate the field measurements (0.5% error). Further analysis of these slight but systematic trends of measurement mismatch should be directed towards expanding the field measurement data set to include more skeletal elements and eliminating potential researcher bias (that is, multiple individuals should take the point cloud measurements).
The measurement results were also compared using a Taylor Diagram. Taylor
Diagrams are commonly employed to evaluate climate model output and are used to graphically summarize how well a model matches observations (Taylor, 2005). In Taylor
Diagrams, the radial axis represents standard deviation. A model is considered representative of reality if it has a similar standard deviation to that observed in nature. The angle of the Taylor Diagram shows the correlation coefficient (R) value between the model and the observation. A higher correlation is Figure 12: Taylor Diagram comparing LiDAR Model with Field Observations. The standard deviation measured in indicated by a lower angle (that is, the the field is shown as a solid line while the model result is shown with a red dot. Since the red dot is close to the x- axis and to the standard deviation of the field result will plot closer to the x-axis on measurements, the LiDAR model correlates well with reality.
16
the Taylor Diagram. Figure 12 shows a Taylor Diagram comparing the measurements
made in the LiDAR point cloud with those made in the field. The solid line indicates the
field standard deviation and the red dot shows how well the model correlates. The R
value of the model is greater than 0.99 and indicates that the model corresponds very
strongly with the data. This indicates that the LiDAR model can be used for further
analysis of the fossils in the Visitor’s Quarry.
V. Discussion
Terrestrial LiDAR’s utility in creating a detail model of the quarry and in allowing for
careful measurement of the gross morphology of the fossils demonstrates that this remote
sensing technique possesses significant potential as a tool in digitizing large-scale fossil
sites. The simple set-up and short collection time for the LiDAR unit allows for field time
to be productively oriented to collecting rich datasets.
a. Orientation of Skeletal Elements in Relation to Death and Taphonomy
The scan data that results from terrestrial LiDAR modeling shows particular potential
in analyzing the relative orientations of skeletal elements. Figure 13 shows a side-by-side
comparison between a photograph of the pectoral girdle of one of the quarry specimens
(Specimen I) and the corresponding LiDAR scan.
Figure 13: Coracoid-Vertebrae Relationship. This composite image shows that the coracoid (labeled B) overlies the vertebrae. This relationship indicates that the organism was preserved lying on its back. 17
Visualization 3 moves anteriorly up the vertebral column of the Speciman I and ends with a sweep of the pectoral girdle. As shown in both the image and the video, the coracoids
(analogous to the breastbone in chickens) overlie the vertebrae. The relationship between the coracoids (labeled B) and the vertebrae in these images was first recognized in the
LiDAR scans and later confirmed with a follow-up visit to the quarry site. This spatial relationship indicates that the organism is lying on its back. Upon further examination of the LiDAR scans, all but one of the individuals in the Fossil Hut were determined to be lying on their backs. Figure 14 shows the quarry interpretation of the majority of the ichthyosaurs lying on their backs.
Figure 14: Skeleton Orientation Interpretation of Visitor’s Quarry. This interpretations shows the individuals in the Quarry in their death orientation. The skeletons have been colorized to show what bones are present (Kelley et al., 2015).
This new information guides the debate over what mechanism ultimately killed the ichthyosaurs. 18
One way that the ichthyosaurs in the quarry could have ended up on their backs is if
they died high in the water column. Ichthyosaurs are top heavy (the majority of the
skeleton is concentrated along their back) with less dense blubbery bellies. If the
ichthyosaurs died high in the water column, then their bodies could have flipped to a
more gravitationally favorable position during the settling process. The flipping of the
body could have been facilitated by the accumulation of gas in the abdominal cavity due
to decomposition. Once the organisms reached the ocean floor below the fair-weather
wave base, they would be outside of the influences of currents strong enough to disturb
the bodies from their arrangement. b. Exhibit Monitoring and Fossil Preservation
Terrestrial LiDAR models also promise to be valuable in the field of site preservation.
Repeated scans over time can potentially be useful in quantifying deterioration of
protective structures (like the concrete wall depicted in Figure 15).
Figure 15: Concrete Retaining Wall in Quarry. This composite image shows a side-by-side comparison of a photograph of a concrete retaining structure in the fossil quarry. This concrete wall supports the unstable slope that the delicate rib bones (upper left corner of the image) are balanced upon. By matching points between the LiDAR model and the photograph in successive scans (taken on a decadal timescale?), the creep of the concrete over time can be quantified and early action can be taken to preserve the rib bones if the wall becomes unstable.
The concrete retaining wall was initially added to the quarry during excavation by
Charles Camp and was later re-cemented by Samuel Wells (Dr. Pat Holroyd, UCMP,
personal communication, July 2015). This centimeter-scale analysis could provide an 19
understanding of what portions of the protective structure are the most susceptible to
cracking and erosion and could allow for proactive countermeasure against failure.
VI. Conclusion
The terrestrial LiDAR model of Berlin-Ichthyosaur State Park demonstranted
qualitative and quantitative success in capturing the large in situ fossil assemblage of S.
popularis. The LiDAR model presented advantages over other techniques in its
portability, speed, and ease with which scans were taken. Although the georeferencing
capability of the GPS unit was limited by the location of the site within a building,
manual registration of the scans was still possible. The holes present in the LiDAR model
result from difficult in getting adequate scan coverage in the affected areas. This lack of
coverage can be remedied by either taking additional filler scans or by integrating the
point cloud with other three-dimensional data sets.
While the overall comparison between the point cloud measurements and the field
measurements was favorable, some measurement bias was observed when the specimens
were sorted by skeletal element. The coracoids were systematically overestimated in the
point cloud while the vertebrae were systematically underestimated. This systematic bias
likely results from one individual making the point cloud measurements. Possible
solutions for this bias include expanding the number of measurements taken to include
more varied skeletal elements and having several individuals make point cloud
measurements.
The LiDAR model shows that the individuals in the Visitor’s Quarry are
predominantly laying on their backs. This death arrangement may indicate that the
organisms died high in the water column (close to the surface) and then flipped during 20 the settling process due to a combination of the force of gravity and the build up of gases in their abdominal cavity. The LiDAR model also have the potential to prove useful in long-term conversation at Berlin-Ichthyosaur State Park.
The construction of this terrestrial LiDAR model represents early work in a large- scale digitization project at Berlin-Ichthyosaur State Park that has employed many different digitization techniques in constructing quarry models. Future work will consist of comparisons of the relative strengths and weakness of the different models (including photogrammetry and structured-light scanning) and of integrating the models into one cohesive data set. The terrestrial LiDAR model of the Fossil Hut quarry at Berlin-
Ichthyosaur State Park demonstrates this technique’s great potential as a tool both scientific research and curational work on large-scale in situ fossils. 21
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Appendix I: Stratigraphic Column of Geologic Units in Berlin-Ichthyosaur State Park Figure 16 shows the stratigraphic units present in Berlin-Ichthyosaur with their corresponding ammonite stratigraphy. The age of the Carnian-Norian boundary is approximately 227 mya.
Figure 16: Stratigraphic Column of Geologic Units in Berlin Ichthyosaur State Park. This figure shows the stratigraphic units present in the park with their corresponding ammonite stratigraphy. The Luning Formation spans the Carnian-Norian Boundary (approximately 227 mya) (modified from Silberling, 1959). 25
Appendix II: Phylogenetic Tree of Ichthyosaurs Figure 17 shows a phylogenetic tree of the supraorder Ichthyopterygia. The branch with the genus Shonisaurus is highlighted in yellow.
Figure 17: Phylogenetic Tree of Supraorder Ichthyopterygia (modified from Motani, 1999). Shonisaurus popularis, the organism of interest in this study, is the only officially recognized species in the genus Shonisaurus. The branch of S. popularis is highlighted in yellow. 26
Appendix III: Schematic of Terrestrial LiDAR Scanner Locations Relative to Major Features of the Fossil Hut
Hut. Figure18
: :
ScannerSchematic. Locations This schematic shows the locationschematic of terrestrialThis scannerthe shows andeach LiDAR for taken in around scan Fossil the 27
Appendix IV: Comparison of Field Measurements with Scan Measurements
Table 1 shows the relationships between field measurements (made with a tape measure and calipers) and measurements taken digitally from the point cloud data.
Table 1: Field Observation vs. Point Cloud Measurements
Field Measurements (cm) Point Cloud Measurements (cm) Specimen I L. Coracoid 48.8 48.4 R. Coracoid 48.9 48.7 R. Mandible 115 113.8 R. Humerus 42.5 41.7 L. Humerus 50.5 52.0 L. Femur 33.4 34.0 Centrum 26.8 23.7 Specimen II Centrum 26.8 24.8 Specimen III Centrum 19 20.8 R. Humerus 31.4 30.8 L. Humerus 29.5 29.9 R. Coracoid 34 41.2 L. Coracoid 34.8 34.9 Speciment IV Centrum 19.3 19.7 R. Humerus 30.8 30.8 L. Humerus 29.1 29.1 Coracoid 29.8 33.8 Mandible 233 236.7 Specimen V Coracoid 33.7 33.9 Humerus 35.8 34.3