www-itg.lbl.gov/Frog -> dsd.lbl.gov/Frog/
The goal of the Whole Frog Project is to provide high school biology classes the ability to explore the anatomy of a frog by using data from high resolution MRI imaging and from mechanical sectioning, together with 3D surface and volume rendering software to visualize the anatomical structures of the intact animal. Ultimately we intend to be able to "enter the heart and fly down blood vessels, poking our head out at any point to see the structure of the surrounding anatomy". A summary of this may be found in: 24 LBL "Whole Frog" Project Summary. EXAMPLE STUDY OUTLINE ON 3D RECONSTRUCTION The secondary goal of this project is to introduce the concepts of modeling and displaying 3D structures directlyfrom 3D images obtained, for example, from MRI imaging (biological specimens), X-ray CT imaging (industrial imaging of non-biological objects), and direct generation from mathematical descriptions. For more information see 25 Geometric Analysis, Visualization, and Conceptualization of 3D Image Data . THE TECHNIQUE FOR ACQUIRING AND PROCESSING THE FROG DATA For a variety of technical reasons relating to differences between mammalian and amphibian physiology, the resolution of MRI images of a frog were not good enough to clearly separate internal structures. A high resolution data set was obtained by a mechanical sectioning technique that gave sufficient resolution to see detail down to the level of large nerves. EXAMPLES OF RECONSTRUCTIONS OF OTHER ORGANISMS High resolution MRI studies of several plants were done as part of this project, with an orange forming the basis of the 3D reconstruction study unit. Slice images are a sequence of sections through the object of interest. These slices may be obtained directly as in mechanical slicing, or by tomographic reconstruction. Themasks are a geometric representation of objects of interest and are obtained by "segmentation" of the images. The slice image files contain all slices for a given organism. For example, the frog slice image data set is 470 x 500 x 1Byte x 136 images. So each 500 bytes from this dataset represents one scan line of the slice image. The images are in 38 Utah Raster Toolkit format, and are available via 39 anonymous ftp. The MRI data corresponding to the section data for the frog is also included. Many of the MRI images (as the tomato is) may require normalization or histogram equalization in order to "see" much in an image displayed on the screen. Both the masks and the data are compressed using the Unix compress utility. Frog/rat/* Note: The orange, tomato, pumpkin, and rat data are only available as MRI - the rat data is not high quality. CREDITS This work was done at Lawrence Berkeley National Laboratory in 1993-1995, and was sponsored at that time by the U. Lawrence Berkeley National Laboratory is operated by the University of California for DOE under contract DE-AC03-76SF00098 Thanks to the many people that made this project possible: LBL Center for Science and Engineering Education * Rollie Otto, Director * Eileen Engel * Summer teachers (TRAC program) + Darrel Richter + V. Padilla + Bea Alexander + Miguel Rivas + Kris Sahu LBL Research Medicine Division (now Functional Imaging Group) * Dr. Tom Budinger (for showing us the potential of high resolution MRI) * Mark Roos and Sam Wong (who did the MRI imaging) * Katie Brennan (for "Fluffy") * Anat Biegon (for the use of her Cryotome) University of California, Berkeley, Biology Dept. Paul Licht (a specialist in amphibian anatomy, for his consulting) * Craig Logan (anatomy student who did most of the frog masks) Computer Science Students * Wing Nip, San Francisco State University (now at Sun Microsystems) Imaging and Distributed Computing Group Staff * David Robertson produced the 45 interactive frog dissection kit * 46 William Johnston conceived and guided the Whole Frog Project. COPYRIGHT NOTICE Copyright 1994 by Lawrence Berkeley National Laboratory The images, data, and documents of the "Whole Frog Project" are copyrighted byLawrence Berkeley National Laboratory. These materials are freely provided for the purpose of scientific research and education by Lawrence Berkeley National Laboratory. Any commercial use of these materials requires prior permissionfrom Lawrence Berkeley National Laboratory.
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