Computer-Enhanced Science Education: The Whole Frog Project
Computers can't teach everything in anatomy, but they can teach some things better, either by themselves or through synergy with conventional methods. Try out this award-winning virtual frog- as a case in point.
"Whole Frog" Project
The ITG "Whole Frog" project is intended to introduce the concepts of
modern, computer based 3D visualization, and at the same time to
demonstrate the power of whole body, 3D imaging of anatomy as a
curriculum tool. 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:
LBL "Whole Frog" Project Summary
.
The secondary goal of this project is to introduce the concepts of
modeling and displaying 3D structures directly from 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. This approach is being developed in
conjunction with summer programs involving high school teachers and
students. For more information see
Geometric Analysis, Visualization, and
Conceptualization of 3D Image 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 mechanical slice data:
For a report on the mechanical sectioning and associated data collection issues,
please see
Whole Frog Technical Report.
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.
Images of reconstructed tomato:
Examples of frog reconstructions:
Example 2 of frog reconstruction. (TIF file)
Example 3 of frog reconstruction. (TIF file)
The following are two different encodings of the same sequence.
MPEG movie of frog rotating (769 KBytes)
Quicktime (JPEG compressed) movie of frog rotating (1,862 KBytes)
Two kinds of data are used in the 3D reconstructions: slice images (example slice),
and masks (example mask). 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.
The masks are a geometric
representation of objects of interest and are obtained
by "segmentation" of the
images. (This can be done manually, or using image
processing techniques.)
The following describes how to get all of the data that went into the images
and reconstructions illustrated in this document.
The "data" behind the 3D models (e.g. of the frog) are images of
slices through the original object, and "masks" that define
various regions of interest (anatomical systems, in the case of
the frog).
-----
Monochrome slice images:
The slice image data are in two different formats:
"raw" (no header) monochrome images with a file
format: each pixel is an unsigned byte, and the scan lines are
stored row-wise. For each data set there is a file called *.hd
that describes the number and size 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.
For example, using PBM:
Get frame one:
rawtopgm 256 256 < tomato.data > frame1
Get frames one to four into a single image:
rawtopgm 256 1024 < tomato.data >frame1-4
Get frame two (skip over all of frame one):
rawtopgm -headerskip 65536 256 256 < tomato.data > frame2
Get frame three (skip over frames one and two):
rawtopgm -headerskip 131072 256 256 < tomato.data > frame3
etc.
These files are available via
anonymous ftp from www-itg.lbl.gov
-----
Color slice images of the frog:
This is the original data obtained by cryotome slicing of the frog. The
images are in
Utah Raster Toolkit
format,
and are available via
anonymous ftp.
-----
MRI data:
The orange, tomato, pumpkin, and rat data are only available as MRI - the rat dataset is not high quality.
The MRI data corresponding to the section data for the frog is also included. However, this MRI
data is also not very high quality. (The speculation is that iron pigments in the frog's
skin interfere with the MRI.)
This data are available via
anonymous ftp.
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. E.g.:
rawtopgm 256 1024 < tomato.data | pgmnorm | your_favorite_display_program
-----
Mask data:
The masks have the same format
and size as the "raw" data and are tar-ed in "*.MASK.tar". Both the
masks and the data are compressed using the Unix compress
utility. (The masks are really one-bit images, but are stored in
8-bit/pixel format. This means that they expand enormously when
uncompressed.)
These files are available via
anonymous ftp.
-----
Misc:
Some Sun rasterfile screen dumps of 3D
reconstructions done by raycasting are stored in
"*.IMAGES.tar".
This is available via
anonymous ftp.
-----
In general, all data may be obtained via anonymous ftp from
www-itg.lbl.gov (128.3.196.93).
- FROG: /pub/Whole.Frog/frog/*
- ORANGE: /pub/Whole.Frog/orange/*
- TOMATO: /pub/Whole.Frog/tomato/*
- PUMPKIN: /pub/Whole.Frog/pumpkin/*
- RAT: /pub/Whole.Frog/rat/*
Note: The orange, tomato, pumpkin, and rat data are only available as MRI - the rat data is not high quality.
This work was done at Lawrence Berkeley National Laboratory in 1993-1995, and was sponsored at that time by the U. S. Dept. of Energy, Energy Research Division,
Mathematical, Information,
and Computational Sciences Division
, John Cavallini program manager.
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. Newton
- Ana L. 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.
- Dr. 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
Copyright (c) 1994 by Lawrence Berkeley National Laboratory
The images, data, and documents of the "Whole Frog Project" are copyrighted by Lawrence 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
permission from Lawrence Berkeley National Laboratory. For further information contact
William Johnston (510-486-5014, wejohnston@lbl.gov).