e-Skeletons: The Digital
Library as a Platform for Studying Anatomical Form and Function
John Kappelman
Principal Investigator
Myriam Zylstra Post Doctoral Project Supervisor
Timothy M Ryan
Graduate Research Associate
Marat Maga Graduate Research Associate
University
of Texas at Austin
I would like to take this opportunity to thank the organizers of this
conference for making it possible for all of us to meet here this week, and
especially Carl Lagoze of Cornell and
Dianne Martin and
Steve Griffin of NSF for all of the hard work that they have put into this
conference.
Today I will update you on the status of our
ongoing digital library project, “eSkeletons”
One of the important goals of
educators is to attempt to ensure that all of our students have the best
possible access to the resources that form the foundation of their learning experiences.
The study of the anatomy is one of the key topics that underlies many
fields within the biological sciences and medicine but has, historically, been
critically dependent upon the availability of actual skeletons for study.
Although much of this study is based on either black and white or
color photographs and drawings, studying actual skeletal elements is an
essential component because it is in this way that the two-dimensional
experience is elevated to the three-dimensional .The quality of the learning
experience is therefore controlled in large part by access to the skeletal
material. Some institutions have excellent skeletal collections, with some
schools having enough extra material that students can check out a skeleton for
home study, while other institutions have no teaching material at all. In the
latter case, students are forced to base their study of the three-dimensional
form and function of the skeleton on two-dimensional pictures from their
textbooks. Clearly, there is little comparability between these two learning
experiences.
PROBLEM:
Uneven access to
the critical laboratory materials used in teaching skeletal anatomy
GOAL:
To provide 1)
the raw materials needed for the study of skeletal anatomy in
2)
a user-friendly learning interface
First, I will discuss the various techniques that
we are using to acquire the raw data that is used to construct the library; and
second I will present the current status of our web interface.
Advances in three-dimensional data capture, display and software
learning interfaces now make it possible to build a digital library of the
skeleton that will serve to even out the disparities that exist among the
learning experiences of students from different institutions.
There are numerous methods now available for digitizing
both the external and internal surfaces of three-dimensional objects. Some of
the most useful technologies for digitizing skeletal materials are three-dimensional
laser scanning and high resolution X-ray computed tomography. Both technologies
are ideally suited for this task because of their noninvasive and
nondestructive natures. These technologies are presently available at the
University of Texas, Austin.
Some of the most recent advances in automated 3-D imaging
incorporate a laser to capture the surface topography of a specimen.
Operating
costs are much lower than CT because laser scanners use standard electric
current, have very low maintenance costs, and do not require a licensed
operator.
The laser scanning technology that we use to capture the
surface geometries of the skeletal elements uses what is known as adaptive
scanning and is manufactured by Digibotics, Inc. of Austin, Texas. This system tightly focuses a laser beam and
uses this single point of light and a triangulation algorithm to measure the
exact x and y coordinates of each point on the surface of the specimen at a
fixed z coordinate level.
The
x, y, z data can be exported to a variety of software programs for wiremeshing
, shading and animation. For the purposes of our Digital Library project, long
scans are usually run overnight or on the weekend, and we have now completed
scans of every element of the human skeleton. We are now completing scans of
the chimpanzee and baboon.
The development of X-ray CT began as a medical diagnostic
tool in 1971 and witnessed a wide number of applications in physical
anthropology. Computerized tomography differs from conventional radiography in
that the X-rays are restricted to a plane and the intensities of the beam,
before and after it passes through the specimen, are measured. Conventional CT
typically has a resolution of 1-2 mm thickness.
High
resolution X-ray CT, also known as industrial CT, offers several advantages over
conventional medical CT. First, HRXCT uses a range of higher energy sources
(typically 125-450 kV) than those available in medical CT, which makes the
instrument capable of penetrating much denser objects including rocks and very
heavily mineralized fossils.
Second,
the X-ray detectors are modular, and these can be switched between linear and
area detector arrays, which increases the resolution of the instrument. The
combination of modular sources and detectors produces a CT system that can scan
a variety of specimens across a wide range of resolutions.
For
example, currently the best resolution available on a medical CT is 1000
microns, while a micro CT can scan as low as 10 microns. This increase in
resolution means that much smaller objects or structures such as trabecular
bone can be clearly imaged.
The
images shown here are those of our recent Hi res X-ray CT of a human
cranium.
3-D Hardcopy Output
Many of the digitizing technologies discussed above come
directly from the fields of computer-aided engineering and manufacturing. In
fact, many laser scanners are specifically designed for reverse engineering and
computer-aided manufacturing (CAM). Once these skeletal elements are digitized,
it is useful to think about the remaining option of outputting these data back
into three-dimensional models for study by a range of students who would not
otherwise have access to the materials.
Automated milling
and stereolithography are two of the best known techniques.
Laser sintering, a process invented by DTM, Inc. is the newest
addition to this line-up of technologies. This process uses a laser to sinter
or fuse nylon or plastic powder into the first layer of the object, which in
turn is sintered to the next layer, and so on, until the 3-D printout is
completed.
Although laser sintering is
relatively expensive at present, it is likely that at some point in the future,
this technology will offer a valuable means for getting replica specimens of
rare, fragmentary, or fragile, or even those of endangered species, into the
hands of students.
The Learning Interface
Archiving skeletal objects themselves as raw data to the
web with no informative or comparative context may prove useful to some
advanced users, but a software interface that serves to teach identifications,
comparative morphology, and anatomical function will certainly serve to extend
the benefits of these data sets to a much larger number of users across all
educational levels. This is the introductory page for our site.
We have designed an interface
that uses an image of the skeleton as a "map" and organizes the
skeletal material by anatomical region.
This site is
constructed with Java script.
Each
region includes color images of each skeletal
element taken from the six standard anatomical views. Each skeletal element has
color overlays of muscle origins, insertion, morphological features and
articular surfaces that can be turned off and on by the user. Higher levels of
detail will include selective micro CT scans of particularly important
anatomical features or elements.
Up to this point the software interface bears a very
close resemblance to what the typical student would encounter in a hard copy
printed book. Where this digital library begins to depart from the typical
anatomy book is with its emphasis on the three-dimensional presentations. Each
skeletal element has both QuickTimeĆ and VRML animations. The former animations
are preset and include rotations around the standard anatomical axes, while the
latter files provide the user with complete control over the anatomical
materials. The VRML files require a more powerful CPU than do the QT animations
and can probably only be accessed by advanced users.
If you are interested, I’ll be showing the QuickTimeĆ and VRML
animations after this session back in the breakout room.
For the purposes
of comparative study, chimpanzee and baboon skeletons will also be posted to
the web site. The interface is constructed in a way that will easily
accommodate other species as well, and we anticipate that, in future years, the
site will be expanded to include other mammalian species as well as other
vertebrates.
An integral component of the user program interface will
include self-evaluation. Virtual anatomy tests will draw from the full range of
materials provided via the 2D and 3D images, as well as database content. They can be presented to the to the student
in the form of multiple choice, matching, and interactive problem solving
questions. Grades can be automatically calculated and reported as the last
screen of the exam for immediate feedback to the student.
The primary audience that the eSkeleton project is aimed
toward is that of college and university students, but we anticipate that the
full range of K through university, or even K through grey learners, will use the web
site. There has, however, been a great deal of interest expressed by potential
users at the high school and middle school levels. In order to respond to this population, we have designed a parallel user
interface that is aimed more directly at the middle school student. This
portion of the web site uses the same basic anatomical data but has a more
"kid friendly" interface. It will also include a number of classroom
exercises that instructors can print out for class activities.
One of the critical issues that has to be addressed is
how to handle the delivery of large
datasets to users. One solution utilized in the design of this project is an
emphasis on client-side storage and interactivity. When the user chooses an element,
all views and overlays for that particular bone are downloaded at once. This
results in a brief download delay initially, however after these images are
stored, the speed of user interactivity is maximized.
Another possible solution that we are investigating is a
CD-web hybrid interface that posts the program instructions to the web site and
delivers the raw data files to the user via a CD ROM. This delivery system
would alleviate unacceptably long download times across low speed networks. In
addition, a separate CD that includes the same information as the web site will
permit the user to access the anatomical data when they do not have web access. It would also
permit updated postings to the web that utilize the same raw data from the CD.
Incompatability between Web browsers has also presented a
problem for data delivery and access for users. At present, we are not aware of
an effective solution to this issue but will probably have to build separate
interfaces for each of the two most popular browsers.
When we started this project we relied on Macromedia’s program
Authorware, a program that we had used to produce virtual laboratories on
CD-ROM. Authorware is not database-friendly over the web, and we switched to
using web authoring software. If anyone
knows of any fixes for Authorware, I’d be very interested in hearing about it.
Being able to quickly search the site for specific information is
another topic that we could use some assistance with re. how to most
effectiveley use metadata.
With
continued agency support, the e-Skeletons project could increase the content of
the database to include detailed information about the skeleton that would
greatly increase its utility. For
example, topics such as diseases of bone, age and growth related changes,
forensic applications, techniques, and case studies and an enlarged archive of comparative taxa.
Moreover, additional high resolution micro CT scans of a
wider variety of skeletal elements
would provide an unparalleled resource not only for scientists in the fields of
anthropology and palaeontology, but medicine as well.
Current web-hosting and address
archiving costs will be on the order of $500-$1,000 per year without any
maintenance or updating. We foresee three options:
1)
It may be possible for the home university to cover these costs.
2) The web site could be migrated to
CD-ROM and distributed by a publisher (who may or may not wish to maintain the
web site).
or
3) ADVERTISING!
CONCLUSION
Archiving anatomical
materials to a digital library will have wide ranging educational implications
because it will make a broad range of study and research materials available to
students of anatomy hailing from a wide number of disciplines, across the K-12
to graduate school levels as well as life-long learners. Providing broad access
to critical materials that are otherwise unavailable to students is one of the
central goals of a national digital library.
Thanks to NSF (IIS and DUE),
and the University of Texas for the support of this project, and Drs. Carl
Lagoze (Cornell), Dianne Martin (NSF DUE) and Steve Griffin (IIS) for inviting
us to this conference.