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PD 3D reconstruction software

merlin merlin at neuro.usc.edu
Fri Jul 2 04:25:56 EST 1993

>Does anybody know about a PD software for 3-D reconstruction of serial 
>sections? The purpose is to reconstruct the organization of larger areas 
>of the CNS, not single neurons.

Perhaps not public domain -- but full source code available without charge
-- and ported to numerous UNIX/X11 architecture machines -- there is a good
contributed code (called the '3dtools toolbox') which runs under the KHOROS
interactive image analysis and display system.  This code can generated 2D
projections of 3D gradient shaded images produced by thresholding a stack
of 2D images.  If you might possibly be interested in this system and you
have the X11 window undump program on your system you can acquire a sample
of five images showing various rotations of a stack 3D MRI scans of a human
head (data acquired from omicron.cs.unn.edu:/pub/softlab/CHVRTD/...) with
enough skull and scalp peeled back to reveal the outermost surfaces of the
human brain.  The combined image is available by anonymous ftp from:


and can be displayed on your X11 server workstation by using this command:

    xwud -in 3D-MRI.xwd

If you are interested in the original data (256 x 256 pixel slices x 16 bit
data points x 109 slices) the original data may be acquired from:


Please note the acknowledgements stored with the original data file if you
wish to reproduce either these images or the original data file.

Alexander-James Annala
Principal Investigator
Neuroscience Image Analysis Network
HEDCO Neuroscience Building, Fifth Floor
University of Southern California
University Park
Los Angeles, CA 90089-2520

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