Virtual Frog Dissection: Interactive 3D Graphics Via the Web

David Robertson, William Johnston, and Wing Nip

Imaging and Distributed Computing Group

Lawrence Berkeley National Laboratory


Published in Proceedings, The Second International WWW Conference '94: Mosaic and the Web, Chicago, IL (1994). Hyperlinks have been updated periodically to replace stale links.

ABSTRACT

We have developed a set of techniques for providing interactive 3D graphics via the World Wide Web (WWW) as part of the ``Whole Frog'' project [ 1 ]. We had three goals: (1) to provide K-12 biology students with the ability to explore the anatomy of a frog with a virtual dissection tool; (2) to show the feasibility of interactive visualization over the Web; and (3) to show the possibility for the Web and its associated browsers to be an easily used and powerful front end for high-performance computing resources.

We have developed techniques to utilize the Common Gateway Interface (CGI) capability of WWW servers to provide an interactive 3D visualization front end through Web clients. These techniques have been used to make a ``Virtual Frog Dissection Kit''. A student using this kit has the ability to view various parts of a frog from many different angles, and with the different anatomical structures visible or invisible. For example, the student can press ``form'' buttons that indicate that he or she wants to view the frog from above, with the exterior and skeleton removed. An advantage to this technique, as opposed to dissecting a real frog, is that undissection is as easy as dissection.

The kit has a forms -based interface. Form submission results in a call to a CGI script, which in turn contacts a continuously running process on a more powerful machine to accomplish the graphics rendering of a large 3D data set representing the frog and its internal organs. The resulting image is converted to Graphics Interchange Format (GIF) [ 2 ] encoding. When that process completes generation of the image, it passes the location of the image file and control back to the script which rewrites the image on the client. While this might sound awkward, the overall process is quite similar to how all rendering systems work, with the image being written into a local frame buffer, or sent across the network as an X-window image.


1. INTRODUCTION

This work is intended to demonstrate three uses for Web technology:

Using a virtual dissection approach provides a realistic representation of the internal 3D structure of animals in a way that physical dissection can only imply: organs and structures may be examined in their undisturbed relationships to each other. One can look at the stomach and skeleton by themselves, with their original relationship to each other, and then add the small intestine to see where it fits in (see Figure 1 ). These operations would be difficult if not impossible in an actual dissection.

Obtaining a 3D data set that represents the internal structures of an animal starts with building a voxel data set (voxels are small cubes - the 3D equivalent of pixels) that can be used as input for surface and/or volume rendering software. Generation of this data set for a frog required mechanical sectioning. Magnetic resonance imaging did not provide sufficient resolution, due to differences between mammalian and amphibian physiology. Each slice was photographed and digitized thereby providing a representation of the frog internals as roughly 10,000,000 tiny volume elements. Subsequently, semi-automatic segmentation (isolation and identification of structures) provided a ``mask'' representing each organ. The details are available in the Whole Frog Technical Report [ 3 ].

Given this data set and the graphics tools to interact with and to present it, the Web pages for the dissection kit were developed. They are designed to be usable over low-bandwidth networks, and with a variety of browsers. They are also designed to have a minimal impact on the http server, and on the workstations used to perform graphics rendering.


2. DISSECTION KIT INTERFACE

The pages of the dissection kit are organized into an introductory page and two versions of the interactive forms-based program, along with associated tutorials. The introductory page provides information on, and access points to, the two versions. One version is designed for browsers able to use image mapping (interactive images), and one provides for those browsers that cannot.

The tutorials work through sample sessions. Having a step-by-step tutorial available is a useful addition to documentation pages. The capabilities of the program, as well as the appearance of the user interface after various steps, can be directly demonstrated. Forms were used instead of images of the user interface so that the tutorial will look the same as the interactive program on the platform used.

The original format of the tutorial caused some confusion, as could be inferred from the transfer log (a record of accesses to our http server), and improvements were made. In general, in developing a fairly extensive forms interface, the transfer log is extremely useful in seeing how a program is utilized, and in suggesting improvements.

The first form of the interactive program is brought up through a link from the introductory page. It is a standard HTML file, with a reference to a previously-generated top view of the frog. No other permanent HTML files or GIF images are generated or accessed during any further interaction. All subsequent images are produced in real time.

Figure 1 shows a form as it appears in the image-mapped version. (In the following only the image-mapped version of the program is covered.) This interface provides three ways for the user to interactively learn about frog anatomy: controlling which organs are visible, controlling the angle from which to view the frog, and using a mode of interaction that brings up brief descriptions of the organs seen in the image. In Figure 1 the first two of these options are exercised.

The form settings in the top two rows control which organs are visible. The ``Skin'' menu controls how much of the frog's skin is seen: all, none, or with a window cut in the skin to show the internal anatomy. (No attempt is made to render the muscles, due to difficulties in achieving an accurate mask for them during segmentation of the data set.) Any combination of the organs listed may be chosen for viewing. With some combinations, even if an organ is chosen, it may not be visible because another item (such as the skin) is also chosen.

The organs are color coded to make them readily distinguishable. These do not necessarily reflect the true colors of the frog's organs. The color coding used is listed below the image.

The images of the frog are inline and thus GIF encoded. Even with this form of compression the amount of data to send can be up to 60 kilobytes, which takes about sixty seconds on a 9600 baud modem. The menu immediately to the right of the image can be set to send compressed images of 3 different sizes: up to 5 kilobytes for those with slower connections, up to 20 kilobytes for normal use, and up to 60 kilobytes for high quality.

Clicking on the image yields different results depending on how the menu labelled ``view'' is set. In the default case, clicking on the image near an edge will rotate the frog in that general direction. Clicking near the middle will reset the view to its initial orientation. If there is currently a top view, clicking near the middle will flip the frog over and show a view from below (as in Figure 1).

If the ``view'' menu is set to its other option, clicking on any organs visible in the frog will give a brief description of that organ. Accomplishing the translation from click to organ description is described in the section on image generation.


3. ARCHITECTURE

Figure 2 shows what occurs when a user submits a form on the client. The form settings are passed to a CGI script written in C, running on LBL's Imaging and Distributed Computing Group's http server. The script parses the incoming data and sends the result via a socket to an already running rendering process (server) on a different machine. The load on the http server is minimal; most of the computation is performed on the rendering server.

The load is further spread out by having four different machines available. One of these four machines is chosen at random to perform the rendering, which takes about a second for the standard image size. There has not been a noticeable impact on the performance of these machines, which are regularly used for other purposes by our group (during peak periods in August 1994, there were 5 to 6 accesses causing image rendering per minute).

The rendering server generates an image from the data list representing the frog. The formation of the data list from the voxel and mask data, and the rendering, are described in the next section. The data list, consisting of points and associated surface normals, is about 5 megabytes. It is loaded once upon the instantiation of a rendering process, and is thus either always in memory or swapped out. A full copy of the data list is loaded in each of the four rendering processes.

After the image is generated by the 3D rendering, it is GIF encoded and written to a temporary file. Temporary image files more than a half hour old are purged by a script that runs periodically. The temporary files have a lifetime that long because a person may want to use the ``Back'' capability available on many Web browsers to go back to a previously generated image, and the image may no longer be in cache.

Since many people may be simultaneously accessing the dissection kit, the file name must be unique, or else one person may receive the image from another's form submission. The method chosen for naming is to take the current time in seconds and microseconds, and concatenate it into the temporary file name. This file name is sent back from the rendering process via a socket to the CGI script.

The script prints the form settings and the location of the image file in HTML format to standard output, where it is intercepted by the http daemon and sent back to the client. Before printing the form settings out, the script checks to see if any of them have changed during the current invocation, as a result of rendering or other actions, and updates them as necessary. For example, a form ``reset'' will set all menus and buttons back to their defaults.

Each invocation of the CGI script is completely independent, and thus there is no information saved from one call to the next. However, the viewing transformation matrix used during rendering has to be saved to be able to generate a sequence of gradually changing views, and this viewing matrix has to be maintained for each user. A method used to store information between invocations is to incorporate that information in one of the form names. Information can also be stored in the URL, but that would result in a lengthy string in this case.

In this case, the current transformation matrix is encoded as a string that is part of a menu name. The CGI script decodes it and passes it to the rendering server, which may modify the matrix. After rendering, the transformed matrix is converted back to a string and replaces the previous menu name when the form settings are sent back to the client.


4. IMAGE GENERATION

An image of the frog is rendered from a pre-existing list consisting of voxel locations and associated surface normals, representing the organs of the frog. The list was produced using a modification of the Dividing Cubes method [ 4 ] for 3D surface generation. Mask values resulting from organ segmentation are used instead of thresholding to identify the voxels that will be utilized in the surface generation step. The modified Dividing Cubes algorithm is used separately on each organ mask, resulting in lists of voxels for each organ. Since the list is only generated once, time is not a factor. Enhancements were made to the way surface voxels are chosen and to the way surface normals are approximated.

The resulting point list contains approximately 450,000 points. If an organ is not selected for viewing, its portion of the point list is skipped. Rendering is straightforward, using a z-buffer for hidden surface removal [ 5 ] ]. A limitation of the current method is that the sub-cubes portion of the Dividing Cubes algorithm is not implemented; the size of the resulting image is dependent on the original data resolution. To use the current method, data sets should be at least 256x256x128.

The use of point (voxel) primitives and previously generated normals results in rapid image generation (one second or less for the standard-sized image) with a good level of detail. Since the image contains much constant background, especially if only a few organs are selected, the GIF method of encoding provides a compression ratio of at least 4:1.

Transmission of the compressed image over a slow network can cause delays. However, those browsers that support ``Back'' and ``Forward'' to go to previously viewed pages, and that support image caching, allow quick viewing of the images that have been generated in the last half hour (older images are purged).

While rendering is occurring, an additional technique is used to enable the ``image click to organ translation'' feature described in a previous section. Analogous to a z-buffer, an ``organ buffer'' is used to store the current organ membership for each pixel. When one voxel overwrites another via the z-buffer method, the organ buffer is updated as well. This technique makes organ identification possible regardless of the orientation of the view: any visible part of the organ will be identified by this technique.

If the interface has just been placed in organ mode (as opposed to rotation mode) the organ buffer is written to a temporary file. Further clicks on the image will result in the CGI script seeking to and reading the appropriate value from that file, instead of contacting a rendering server to generate a new view. The seek location is given by the clicked-on x and y position. Note that the configuration file typically associated with image-mapping is not used. With a configuration file, the x and y position are used as an index into a predefined region, and the exact position is not available to the script.


5. CONCLUSIONS

The frog dissection kit is designed to be readily accessible. Consideration is given to the different capabilities of browsers. A non-image mapped version of the interface uses a compass-like control instead of image clicks for rotation. Also, there is an option to generate smaller images for browsers connected over low-bandwidth networks. To facilitate learning the capabilities of the user interface, step-by-step tutorials demonstrating the use of the program are also included.

The virtual dissection kit shows three uses for Web technology:


6. ACKNOWLDGEMENTS

We thank Keshea Williams of Jackson State University, Lynne Ottoson of Oakland Public Schools, and Dennis Herriford of Portland Public Schools, for their input in the development of the dissection kit, and the people who made the ``Whole Frog'' project possible.

This work was sponsored by the U. S. Dept. of Energy, Energy Research Division, Office of Scientific Computing, John Cavallini program manager. Lawrence Berkeley Laboratory is operated by the University of California for DOE under contract DE-AC03-76SF00098.

This paper is available as a technical report, LBL-36152, University of California, Lawrence Berkeley Laboratory, Berkeley, CA 1994.


7. REFERENCES

1. Johnston, W.E. The Whole Frog Project (Web page). http://froggy.lbl.gov/, University of California, Lawrence Berkeley Laboratory, Berkeley, CA, 1994.

2. Graef, G. Graphics formats: A close look at GIF, TIFF, and other attempts at a universal image format. Byte 14 9 (Sept. 1989), 305-310.

3. Nip, W. and Logan, C. Whole Frog Technical Report. LBL-35331, University of California, Lawrence Berkeley Laboratory, Berkeley, CA, 1991.

4. Cline, H.E., Lorensen W.E., Ludke, S., Crawford, C.R., and Teeter, B.C. Two algorithms for the three-dimensional reconstruction of tomograms, Medical Physics 15 3 (May/June 1988), 320-327.

5. Foley, J.D., and van Dam, A. Fundamentals of Interactive Computer Graphics, 2nd ed., Addison-Wesley Publishing Company: Reading, MA, 1990.




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Page last modified: 01/09/05
Contacts: Bill Johnston, David Robertson