PD 3D reconstruction software

& Schwartz eric at thing4.nntp-read.bu.edu
Mon Jul 5 13:19:14 EST 1993


In article <20uln0$qt3 at mailgzrz.TU-Berlin.DE> nevr2134 at mailszrz.zrz.tu-berlin.de (Joachim Erber) writes:


>   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.


   Thank you
		   Daniel Faensen

			__o
		       ~\<,

It may be possible for you to adapt general purpose visualization
software for anatomical data. One system available on the net is
khoros which can be found at many sites (use archie) or:
ftp.uu.net:pub/window-sys/khoros.  Another is AVS, which is licensed.
These systems have general support for voxel and polyhderal based
modeling, but are oriented towards visualiziation of surfaces which
are obtained from analytic or numerical models (e.g. iso-potential
surface, etc). Brain data, in my experience tends to be much more
complex, and the algorithms which are used in these systems (such as
marching cubes) to provide a polyhedral model from a voxel model may
not produce strictly correct results.  "Correctness" may or may not be
an issue for you: If your goal is simply to visualize data, it may not
be necessary for the full details to be "correct". However, if your
goal is to perform measurements on the data, correctness becomes more
critical. For example, if your goal is to flatten a cortical surface,
a single incorrect edge linking nodes on two adjacsent banks of cortex
can cause a catastrophic failure of later algorithms.
 
We have a system of computer aided neuroanatomy that is in the final
stages of beta testing, and which was designed with the goal of
measurement, rather than simple "eyeballing" data. This system will be
released publicly in early September.  It provides support for image
processing of serial sections, three dimensional reconstruction of
serial sections at the voxel level, "brain peeling" of the 3D models
(i.e. digital production of tangential sections of the 3D model),
"brain flattening" (optimal 2D representation of 3D cortical
surfaces), and other utilities and functions.  Also supplied with this
system is a test data set consisting of coronal sections of a Macaque
brain (one-eye enucleated for one month prior to sacrifice), stained
for cytochrome oxidase, and fully processed with all aspects of our
system (e.g. 3D reconstruction, flattening, texture mapping of stain
density in 3D and 2D, etc.).


I would encourage anyone interested in receiving a copy of our system
to send me e-mail indicating so. I will send back instructions on ftp
access to our system as soon as it is ready for public release.
My e-mail and surface mail addresses are listed in the sign off to
this note.
 
The following papers describe this system.
 
GENERAL OVERVIEW:
@article{Schwartz88Computational,
   author = {E. L. Schwartz and B. Merker and E. Wolfson and A. Shaw},
   journal = {IEEE Computer Graphics and Applications},
   number = {4},
   pages = {13-28 (July)},
   title = {Computational neuroscience: Applications of computer graphics and image processing to two and three\ dimensional modeling of the functional architecture of visual cortex},
   volume = {8},
   year = {Schwatzr1988},
   keywords = {CGA 1988}
}
BRAIN FLATTENING:
@article{Schwartz89Numerical,
   author = {E. L. Schwartz and A. Shaw and E. Wolfson},
   journal = {IEEE Trans. Pattern Analysis and Machine Intelligence},
   pages = {1005-1008},
   title = {A numerical solution to the generalized mapmaker's problem},
   volume = {11},
   year = {1989},
   keywords = {PAMI }
}
 
@article{Wolfson89Computing,
   author = {E. Wolfson and E. L. Schwartz},
   journal = {IEEE Trans. on Pattern Analysis and Machine Intelligence},
   pages = {1001-1005},
   title = {Computing minimal distances on arbitrary polyhedral surfaces},
   volume = {11},
   year = {1989},
   keywords = {PAMI}
}
POLYHDERAL MODELING:
@article{Shaw89Construction,
   author = {A. Shaw and E. L. Schwartz},
   journal = {SPIE Medical Imaging III: Image Capture and Display},
   pages = {221-233},
   title = {Construction of polyhedral surfaces from serial sections: exact and heuristic solutions},
   volume = {1091},
   year = {1989}
}
VOXEL MODELING:
@article{Frederick90Brain,
   author = {C. Frederick and E. L. Schwartz},
   journal = {Visual Computer},
   number = {1},
   pages = {37-49},
   title = {The brain peeler: viewing the inside of a three dimensional shell},
   volume = {6},
   year = {1990}
}
 
Best regards,
Eric
________________________________________________________
| Eric L. Schwartz                                     | 
| email: eric at thing4.bu.edu                            |
| Office: (617)353-6179 ;  FAX: (617)353-6178          |
| Prof. of Cognitive and Neural Systems                |
| Prof. of Elec. Engineering and Computer Systems      |
| Prof. of Neurobiology                                |
| Surface Mail: Dept. of Cognitive and Neural Systems  |           
| Boston University                                    |
| 111 Cummington Street::Boston MA. 02215              |
|______________________________________________________|
--
Best regards,
Eric
________________________________________________________
| Eric L. Schwartz                                     | 
| email: eric at thing4.bu.edu                            |
| Office: (617)353-6179 ;  FAX: (617)353-6178          |
| Prof. of Cognitive and Neural Systems                |
| Prof. of Elec. Engineering and Computer Systems      |
| Prof. of Neurobiology                                |
| Surface Mail: Dept. of Cognitive and Neural Systems  |           
| Boston University                                    |
| 111 Cummington Street::Boston MA. 02215              |
|______________________________________________________|



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