reprinted from T. Rowe, W. Carlson, and W. Bottorff, 1993. Thrinaxodon: Digital Atlas of the Skull. The University of Texas Press. CD-ROM.



Department of Geological Sciences and
Vertebrate Paleontology Laboratory
The University of Texas at Austin
Austin, Texas 78712


This disc is the result of two ongoing research programs at the University of Texas and private industrial research and development efforts elsewhere in Austin. One of the UT research programs is aimed at testing a wide range of analytical technologies for problems in mineralogy and petrology (e.g., Carlson and Denison, 1992). The other is directed at exploring various digital technologies potentially useful to systematists and morphologists studying skeletal tissues in modern and extinct vertebrates (e.g., Bottorff and Rowe, 1989).

One of the Texas industrial research and development efforts is in the field of computed X- ray tomographic (CT or CAT) scanning. CT scanning is a standard medical diagnostic tool used for more than two decades to image the human skeleton and other tissues. For nearly a decade medical scanners periodically have been applied to fossils, with considerable success for human-sized (and somewhat larger) vertebrates (e.g., Conroy and Vannier, 1984). Scientific Measurement Systems (SMS) of Austin has recently developed a CT scanner that can achieve two orders of magnitude finer resolution than is generally possible with medical scanners, while also successfully imaging a much wider range of materials. This opens the door for the first time to imaging skeletons of the huge diversity of both modern and fossilized taxa that lie within the smallest order of vertebrate size magnitudes.

This stunning new technology is the basis for our reanalysis of the fossil Thrinaxodon, an extinct relative of modern mammals that has figured importantly in understanding the early history of mammals (e.g., Rowe, 1993).

Another technology central to this research is CD-ROM. A major goal in our tests of modern digital technologies in Earth Sciences has been to evaluate potential methods for distributing the data generated by these new tools. In the two decades that CT scanning has been applied to skeletal tissues, only a tiny fraction of the expensive data generated has been archived or distributed for general use by the research and educational communities. Most of what has been distributed is recorded on film instead of in its native digital format. Until now, visualizing original digital CT imagery required powerful, expensive computational facilities with large volumes of storage space. Typically, suitable equipment has been found only on-site with the CT scanner itself, usually a medical imaging center. CT scanning has yet to fulfill its potentially revolutionizing power for research because, in the absence of a feasible method to disseminate and archive the large volumes of digital data produced by this technology, it has served only a small fraction of the interested scientists. CD-ROM has emerged during the last two years as the first seemingly practical method for publishing large volumes of digital data, as the costs of mastering compact discs dropped dramatically and as inexpensive computers capable of visualizing CT imagery and using CD-ROMs have become widely available.

The willingness of Scientific Measurement Systems to provide us imagery in easily exportable file formats was another key component in the success of this project. The entire results of the CT analysis, a total of 767 separate CT images plus several thousand images that animate visual passage through the skull are presented on this disc in formats designed to facilitate rapid inspection and comparison. We anticipate that this combination of technologies will provide a tool of unprecedented power and informativeness for systematists and other biologists interested in hard tissues, and a model for other scientific studies as well.

The collaboration of the University of Texas Press was a last key element in this project. The UT Press solved a host of publication issues relating to copyright of digital media, reproduction permissions for older literature that is included on the disc, and distribution of the disc. Without that assistance, the publication of this unique data set and the accompanying research library on CD-ROM would not have been possible.


Thrinaxodon was an ideal test of ultra high resolution CT scanning for imaging small fossils because it is already comparatively well known. For more than a century it has played a highly significant role in understanding the evolution of mammals from more primitive cynodonts, and the full range of techniques available to paleontologists has been applied to it. Thrinaxodon has been studied in great detail from mechanically sectioned specimens by Everett Olson (1944) and Steve Fourie (1974), and from acid and mechanically prepared whole specimens that represent a range of ontogenetic stages by F. Rex Parrington (1946), Richard Estes (1961), and A. W. Crompton (1963). The study by Fourie (1974) was especially thorough, being based upon serial sections of an entire specimen made at 200-micron intervals in the coronal (vertical) plane, and it provided an exceptionally detailed control for evaluating the CT imagery of Thrinaxodon provided on this disc.

An excellent adult specimen, previously described and figured by Richard Estes (1961), was kindly made available to us by the Museum of Paleontology and the University of California, Berkeley (UCMP 40466). The SMS scanner was able to image the specimen at 200-micron slice thicknesses, duplicating or exceeding the resolution of earlier studies using mechanical techniques (Olson, 1944; Fourie, 1974). The SMS scanner also provided substantially greater precision in the measurement and calibration of successive sections than was possible with mechanical techniques. Figure 1 of this INTRODUCTION presents examples of sagittal, coronal, and transverse CT images, with a key to distinguishing bone, matrix, sutures, and natural cavities in the bone. The entire CT data set is accessible from the MAP screen.

Two groups of articles are included on this disc to aid readers in interpreting CT imagery and in understanding the anatomy and importance of Thrinaxodon. The first group describes some technological aspects of this disc. In A Brief Introduction to Computed X-ray Tomography, William Carlson presents discussions of the fundamentals of X-ray CT imaging, what a CT image shows, and some complexities and limitations of CT imaging. William Bottorff presents a summary of image format technical specifications that will assist researchers in manipulating these data for their own research interests long after the software that runs this application is obsolete. A short overview of how these data were converted and mastered onto CD-ROM is presented below, as part of this Introduction to the Digital Atlas.

As an additional aid to readers in evaluating the capabilities of this technology, making this study of Thrinaxodon truly comprehensive and taking advantage of the large storage volume of CD-ROM, we have also included a reference library of digital editions of the classic literature on the anatomy of Thrinaxodon. The republished works include Everett Olson's (1944) classic monograph on "The Origin of Mammals Based on Cranial Morphology of the Therapsid Suborders," in which Thrinaxodon was among a number of fossils serially sectioned in one of the most extensive comparative studies ever to use mechanical sectioning techniques. Also included is Steve Fourie's (1974) detailed study of Thrinaxodon based on serial sections, Richard Estes' (1961) study of a growth series of Thrinaxodon that includes the specimen imaged on this disc, and A. W. Crompton's (1963) definitive study of tooth replacement in Thrinaxodon.

Lastly, fifty years after conducting the first serial section research on Thrinaxodon, in the Foreword to this disc Everett Olson sets out a context for evaluating this technology by placing computed tomographic scanning and CD-ROM in the light of a brief history of serial sectioning of fossils for comparative evolutionary studies.



MAP: This is a navigational map for the entire interactive portion of the disc; users can jump directly to any part of the disc from the MAP and return to the MAP from any screen.

SECTIONS MENU: This menu accesses all serial section stacks. It is accessed from the MAP and from most screens showing individual serial sections.

CONTENTS: Within each stack is a series of CONTENTS screens that show postage-stamp-sized images of every fifth slice in that stack. Clicking on an image with a mouse provides instant access to that slice. CONTENTS screens are accessible from every screen showing individual serial sections.

ANIMATION MENU: This menu accesses all flics or animations; clicking on a flic button plays the animation once and returns the user to the ANIMATION MENU. This menu also accesses ANIPLAY, a publicly distributable animation player by AUTODESK, Inc. (originally distributed under the name AAPLAYHI), for interactive and repetitive viewing of all flics. A text file, ABOUT ANIPLAY, is accessible from the ANIMATION MENU and describes the operation of this simple program. The ANIMATION MENU is accessible from the MAP screen and most screens showing individual serial sections.

To run ANIPLAY at proper screen configuration, it is necessary to load one of the VESA drivers that are distributed with that program. Several are included here and support a range of video adapters. These are loaded into a VESA subdirectory [C:\THRINAX\VESA] that is set up on your hard drive during the installation procedure for this disc; they must be loaded from DOS before starting the Digital Atlas. This procedure is not necessary to trigger flics using buttons in the Digital Atlas; it is only needed if you wish to interactively use the animations from ANIPLAY.

TEXT MENU: This menu accesses the library of text documents on the disc. It is accessed from the MAP and from most other screens. (Additional text files on bibliographic and copyright information are in the root directory of the disc, accessible through DOS commands.)


These stacks contain contiguous 200-micron- thick CT slices of the skull of Thrinaxodon, made along the three orthogonal anatomical axes, by Scientific Measurement Systems of Austin. These slices comprise a digital three-dimensional density map of the skull of Thrinaxodon. They include 154 transverse (horizontal) slices, 366 coronal (vertical), and 247 sagittal slices. Slices are consecutively numbered within each stack.

Hyper buttons connect consecutive slices and permit both forward and backward movement through the stacks of sections. The disc contents can thus be followed much as one navigates through a collection of conventional histology sections mounted on microscope slides. Users can move through each stack one slice at a time (in 200- micron intervals) or five slices at a time (in 1- mm intervals). Additional hyper buttons provide access to the major navigational screens described above.

CONTENTS screens for each serial section stack permit rapid jumps to particular slices anywhere within the stacks. Every fifth slice is linked to anatomical labels of that image.

ANATOMICAL LABELS are available for every fifth slice and are accessed with a hyper button. From each screen displaying labels, a pop-up, scrollable abbreviation key appears via another hyper button.


Nine animated flip-books, known as "flics," scroll through the consecutive CT slices of the skull in different planes and magnifications. One flic is included with each serial section stack and is accessible from every slice screen in that stack (this is the only flic directly accessible from a slice screen). Flic frames are each numbered, linking them to specific slices in the serial section stacks. Clicking the "Flic" button on any screen in a stack plays the flic for that stack. When the animation is over, the user is returned to the same screen from which the flic was triggered. Flics offer a novel method of visualizing detailed anatomy of the skull, permitting users to rapidly orient a particular slice within the three-dimensional framework of the entire skull. They also enable rapid location of individual structures and slices of interest.

One additional flic, 3D_SKULL, shows the external anatomy of the entire skull. It is triggered from the ANIMATION MENU or interactively through ANIPLAY.

The ANIMATION MENU provides access to all animations, including close-up flics of the braincase and snout in sagittal, transverse, and coronal views that are not accessible from slice screens.

The interactive program ANIPLAY, by AUTODESK, Inc., is also included on the disc to enable interactive viewing of the flics. From ANIPLAY, flics can be viewed one frame at a time or in continuous loops that can be played at variable speeds. ANIPLAY is accessible from the MAP screen and from the ANIMATION MENU screen. Information about ANIPLAY is available in a text file accessed by a button on the ANIMATION MENU.



1) FOREWORD ............... Everett C. Olson, 1993

2) INTRODUCTION TO THE DIGITAL ATLAS ....................... Timothy Rowe, 1993

3) A BRIEF OVERVIEW OF COMPUTED X-RAY TOMOGRAPHY, ................. William D. Carlson, 1993




6) TOOTH REPLACEMENT IN THE CYNODONT REPTILE THRINAXODON LIORHINUS ................. Alfred W. Crompton, 1963 (Reprinted from the Annals of the South African Museum)

7) CRANIAL ANATOMY OF THE CYNODONT REPTILE THRINAXODON LIORHINUS ...................... Richard Estes, 1961 (Reprinted from Bulletin of the Museum of Comparative Zoology, Harvard University)

8) THE CRANIAL ANATOMY OF THRINAXODON LIORHINUS ....................... Steve Fourie, 1974 (Reprinted from the Annals of the South African Museum)

9) THE ORIGIN OF MAMMALS BASED UPON THE CRANIAL MORPHOLOGY OF THE THERAPSID SUBORDERS ................... Everett C. Olson, 1944 (Reprinted from Special Papers of the Geological Society of America)

10) ON THE CRANIAL ANATOMY OF CYNODONTS .............. Francis R. Parrington, 1946 (Reprinted from the Proceedings of the Zoological Society of London)

Complete, duplicate versions of these articles with their illustrations are stored in the DOCUMENT subdirectory of the ARCHIVE directory of the disc. Text is stored in two formats. Files with the .TXT extension are ASCII files that can be loaded into virtually any word processor. Those with the .DOC extension are formatted for Microsoft WORD (2.0) for WINDOWS. Also stored in the DOCUMENT subdirectory are the original scanned image files. They are stored in either .PCX or .TGA format, depending on whether the original published illustrations were line drawings or photos.


MEDIA MASTER (distributable run-time version), by VISION IMAGING, 10231 Slaughter Avenue, Suite 112, Fountain Valley, CA, 92708. Media Master software was used to build and access the interactive files and animations on the CD. A run-time version is included on the disc, providing users all software necessary to use the information on the disc.

ANIPLAY (originally named AAPLAYHI), by AUTODESK, Inc., 2320 Marinship Way, Sausalito, CA 94965. Animator Pro software by AUTODESK, Inc. was used to build the animations (flics) included on the disc. AAPLAYHI is a freely distributable player for animations produced with Animator Pro software. It offers interactive control (variable speed play, frame-by-frame play) of .FLI and .FLC files.


The ARCHIVE directory contains all of the source files that were used to build this disc. The ARCHIVE directory is accessed through standard DOS commands. This directory was not designed as an interactive part of the disc, although the images and animations stored in the directory are accessible from the Digital Atlas from ANIPLAY. Subdirectories within the ARCHIVE directory contain all of the raw .TIF files that were generated by the Scientific Measurement Systems CT Scanner. Also included are text files.


The data on this disc are organized under the ISO 9660 standard, for use on PC computers.

The basic text and image data are stored in standard formats that can be exported to other environments and applications for digital analysis. All text is stored as ASCII files with a .TXT file extension. Imagery is stored in both the original .TIF format generated during CT sectioning (in the ARCHIVE directory) and in .TGA format (in the THRINAX directory). The latter files were converted from .TIF files by Media Master and are rescaled versions of the original images. Media Master flips the pixel values of these files in a way that may not be properly read by some imaging software that generally supports the .TGA format. The original .TIF files do not suffer this problem. See the analysis by William Bottorff for a discussion of these file formats.

Animations are stored as .FLC files viewable at standard VGA screen resolutions of 640 x 480 pixels. In the ARCHIVE directory are .FLI versions of most animations which can be viewed on low-resolution screens.




All of the CT images included on this disc were converted from a binary format to gray scale .TIF files using proprietary image conversion software developed by Scientific Measurement Systems, Inc., of Austin, Texas. These images are included in .TIF format in a separate ARCHIVE directory that is accessible using standard DOS commands; it is not part of the interactive portion of this disc. The .TIF files were converted to flipped .TGA files by the Media Master multimedia authoring software used to build the interactive application that comprises the bulk of this disc. This conversion was a mandatory requirement of Media Master.


All of the previously published literature in the REFERENCE LIBRARY was converted to ASCII text for inclusion on this disc. This was done using the optical character recognition software WORDSCAN PLUS (International Version) from Calera Recognition Systems (copyright 1991). This software was used with a Hewlett Packard Scanjet flatbed scanner interfaced to a Hewlett Packard QS/20 (80386) PC computer. The initial phases of proofing and error correction were made with WORDSCAN PLUS, whereas final corrections and indexing were done using WORD for WINDOWS.


Text figures from republished literature were scanned using the HP SCANNING GALLERY software that is distributed by Hewlett Packard with its Scanjet flatbed scanner. Each image was then imported for correction into PC PAINTBRUSH for WINDOWS, a program that is distributed by Microsoft as a part of its WINDOWS 3.1 software. The scanned images typically required manual relabeling and "cleaning" of some lines and background to be made suitably legible for digital publication. In some instances, we were forced to separate drawings that were originally clustered together into a single figure and place them on separate screens. This necessary in order to assure that each individual drawings would be sufficiently large and legible to be usefully viewed on a computer screen.


Original text files were generated using the word processing packages WORD FOR WINDOWS and WORD for Macintosh, from Microsoft.

Animations were built using AUTODESK ANIMATOR PRO software from AUTODESK, Inc. (version 1.0 for DOS 386 or 486 computers, copyright 1991). This software package also supplied the program AAPLAYHI (renamed ANIPLAY on this disc) that is one of two animation players that are included on the disc.

Composite images, such as those in the CONTENTS screens and the ANIMATION MENU were made using RIO image design and presentation software from Graphic Software Labs. We ran RIO on the ATVista graphics board from Truevision, installed in a PC 80486 computer with 16 megabytes of RAM and a 1.2 gigabyte hard disc.


MEDIA MASTER MULTIMEDIA AUTHORING SOFTWARE by Vision Imaging (copyright 1991) was used to build the interface that connects all of the individual CT images, the animations, the text files, and the text figures. MEDIA MASTER includes its own animation player as well as permitting linkage with ANIPLAY by AUTODESK. Media Master also provides a presentation mastering program that assembled these materials into a format suitable for publication on CD.


Pre-mastering of several prototype CD-ROMs used for testing was done using ROMMAKER software from JVC, together with the PERSONAL ROMMAKER hardware, a device that prints individual ISO 9660 CD-ROMs. A "one-off" CD-ROM built with the JVC ROMMAKER was sent to Nimbus Information Systems for final mastering and replication.


Bottorff, William W., and Timothy Rowe 1989. Images for Natural History. Cadence, May 1989: 105-108.

Carlson, William D., and Cambria Denison, 1992. Mechanisms of porphyroblast crystallization: Results from high-resolution computed X-ray tomography. Science, 257 (28 August, 1992): 1236-1239.

Conroy, Glenn C., and Michael W. Vannier, 1984. Noninvasive three-dimensional computer imaging of matrix-filled fossil skulls by high-resolution computed tomography. Science 226 (26 October, 1984): 456-458.

Crompton, Alfred W., 1963. Tooth replacement in the cynodont reptile Thrinaxodon liorhinus. Annals of the South African Museum 46: 479- 521.

Estes, Richard, 1961. Cranial anatomy of the cynodont reptile Thrinaxodon liorhinus. Bulletin of the Museum of Comparative Zoology (Harvard University) 125: 165-180.

Fourie, Steve 1974. The Cranial anatomy of Thrinaxodon liorhinus. Annals of the South African Museum 65: 337-400.

Freiwald, Leah, and Lee Marrs, 1990. Inside Autodesk Animator. New Riders Publishing, Thousand Oaks, California (ISBN 0-934035-76- 8).

Helgerson, Linda W., 1992. CD-ROM. Facilitating electronic publishing. VNR Computer Library, Van Nostrand Reinhold, New York, New York (ISBN 0-442-00523-7).

Olson, Everett C., 1944. The origin of mammals based upon the cranial morphology of the therapsid suborders. Special Papers of the Geological Society of America No. 55: 1-136.

Parrington, Francis R., 1946. On the cranial anatomy of cynodonts. Proceedings of the Zoological Society of London 116: 181-197.

Rowe, T. 1993. Phylogenetic systematics and the early history of mammals. In: Mammal Phylogeny, edited by F. S. Szalay, M. J. Novacek, and M. C. McKenna, volume 1, pp. 129-145. New York, Springer Verlag.