Visible Human, Construct Thyself:
The Digital Anatomist Dynamic Scene Generator
James F. Brinkley, Evan M. Albright, Sara Kim, Jose L.V. Mejino, Linda G. Shapiro, Cornelius
Rosse
Structural Informatics Group, Department of Biological Structure,
University of Washington, Seattle, WA
brinkley@u.washington.edu
Availability of the Visible Human dataset has led to
many interesting applications and research projects
in imaging and graphics, as evidenced by the Visible
Human web site and by papers from the previous
conference. However, the project has not yet
achieved the long-term goal stated in the Visible
Human Fact sheet, to “…transparently link the print
library of functional-physiological knowledge with
the image library of structural-anatomical
knowledge into one unified resource of health
information.”. We believe that the critical missing
pieces necessary to achieve this goal are 1) a
comprehensive symbolic knowledge base of
anatomical terms and relationships that gives
meaning to the images, 2) a fully segmented dataset
that is widely available and that associates each
voxel or extracted structure with a name from the
knowledge base, and 3) methods for combining
these resources in intelligent ways.
In a companion paper, we propose that the Digital
Anatomist Foundational Model (FM) has the
potential to become the required symbolic
knowledge base[Rosse2000]. We are also aware of
many efforts to segment the VH data, although none
of these efforts has yet resulted in widely available
segmented data.
In this paper we assume that the required resources
are or will become available. Instead we concentrate
on the third critical piece, namely, methods for
combining the resources in intelligent ways. We
describe the Digital Anatomist Dynamic Scene
Generator, a Web-based program that uses the FM
to intelligently combine individual 3-D mesh
“primitives”, representing parts of organs, into 3-D
anatomical scenes. The scenes are rendered on a
fast server, the rendered images are then sent to a
web browser where the user can change the scene
or navigate through it.
The Dynamic Scene Generator. The scene
generator is composed of several modules from our
Digital Anatomist Information System (AIS), a
distributed, network-based system for anatomy
information [Brinkley1999].
Web
Web Browser
Browser
CGI
CGI Script
Script
FM
FM Server
Server
Graphics
Graphics Server
Server
“Data
“Data Server”
Server”
FM
FM
3-D
3-D
Primitives
Primitives
Correspondences
Correspondences
Figure 1. The Digital Anatomist Dynamic
Scene Generator modules.
The building blocks of a scene are shown in the
bottom row, and consist of terms and
relationships from the FM, 3-D mesh
primitives, and a list of correspondences
between the primitives and names in the FM.
These resources are made available by means of
the FM Server and the Data Server (which for
now is simulated by a function that accesses a
flat file).
Scenes are generated and rendered by the
graphics server, currently running on an Intel
Quad Processor. The graphics server accepts
commands from perl CGI scripts that
implement three different user interfaces: an
authoring interface for creating new scenes, a
scene manager for saving and retrieving scenes,
and a scene explorer for end users. These
interfaces generate web forms which capture
user commands to add structures to a scene, to
save a scene, to rotate a scene, etc. These
commands are in turn passed to the graphics
server, which performs the action, renders the
scene, and returns an image snapshot to the web
browser, along with forms allowing further
interaction. Screenshots of the three interfaces are
shown below:
Figure 2. The authoring interface, displays a frame
for navigating through the FM, and for selecting
structures to add to the scene. It also allows queries
of the FM so that entire subtrees (e.g. all parts of the
Descending thoracic aorta) can be added,
highlighted or removed.
Figure 3. The scene manager interface allows the
author to create scene groups, consisting of initial
scenes and “add-ons”, which are subscenes that can
be added to an initial scene in the end-user interface.
Once a scene group is created, it is immediately
available to the scene explorer.
Figure 4. The end user scene explorer presents
a list of structures in the scene that can be
selected, then removed or highlighted. It also
shows the available add-ons as small icons that
can be added by the user. As on the other
interfaces, camera controls allow the scene to
be rotated or zoomed.
Plans and Discussion. We are currently
performing a preliminary evaluation of this
system, to see how the scene generator can be
used as an educational tool for anatomy
teachers and students. Feedback from this and
other evaluations will help us combine 3-D
scenes with 2-D annotated images to create a
distance learning module in anatomy. In the
longer term, the resulting information system,
when filled out with segmented models from
the entire Visible Human, has the potential for
many other Web-based applications, including
structure-based visual access to non-image
based biomedical information, thereby bringing
us a step closer to the long term goals of the
Visible Human Project.
Acknowledgements. This work was supported
by NLM Grants LM06316 and LM06822.
References
[Rosse2000] Rosse, C., Mejino, J. L., Shapiro,
L. G. and Brinkley, J. F., "Visible Human,
Know Thyself: The Digital Anatomist
Structural Abstraction," in Visible Human
Project Conference 2000. Bethesda, Maryland:
National Library of Medicine, 2000 Submitted.
[Brinkley1999] Brinkley, J. F., Wong, B. A.,
Hinshaw, K. P. and Rosse, C., "Design of an
anatomy information system," Computer
Graphics and Applications, vol. 19, pp. 38-48,
1999.