reprinted from T. Rowe, W. Carlson, and W. Bottorff, 1993. Thrinaxodon: Digital Atlas of the Skull. The University of Texas Press. CD-ROM.
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decades that CT scanning has been applied to skeletal tissues, only a tiny fraction of the expensive data generated has been archived or distributed for general use by the research and educational communities.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.
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.
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.)
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.
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.
2) INTRODUCTION TO THE DIGITAL ATLAS ....................... Timothy Rowe, 1993
3) A BRIEF OVERVIEW OF COMPUTED X-RAY TOMOGRAPHY, ................. William D. Carlson, 1993
4) DIGITAL IMAGERY: FILE FORMATS, CONVERSIONS, AND FUTURE OPPORTUNITIES FOR MANIPULATION ............. by William W. Bottorff, 1993
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.
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 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.
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.
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.