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PD 3D reconstruction software

Doug Merritt doug at netcom.com
Sun Jul 4 13:05:29 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.

I misread your question and prepared the following info about
a CT package for reconstruction of sections, which apparently is not
what you want. I'll post it anyway in case someone else finds it

If I now interpret your question correctly, you actually want something
to glue sections together into a 3D model, which would involve detection
of object boundaries versus object interiors in the slices, and then
fitting polygons or some kind of 2d curves to pass through those edges.
The resulting 3d models would then be displayed by some handy rendering

I don't know personally of PD software for that, but if you find some,
I'd caution that you will likely need to fiddle with the edge detection
to fine tune it for your purpose. This is the kind of thing that is
invariably handled by e.g. thresholding heuristics rather than by a
universally robust algorithm. Then again, contrast enhancement followed
by simple thresholding for edge detection isn't all *that* bad
for some purposes.

The actual algorithms used in the naive approach outlined here are
fairly simple and could be hacked together by a local graphics hacker
moderately easily if you fail to find the PD software you want. Hmm,
come to think of it, you should probably read the FAQ's for all the
graphics newsgroups; something like this probably does exist already.

Here's the CT info:

Some years back I found something along these lines available by ftp...
just now I went and found it again to give you exact information,
because it's in an obscure directory if you don't know the author's

	Machine: ftp.apple.com
	Directory: /pub/malcom
	Archive name: ct.tar

        This is a package of code that accompanies the book
        "Principles of Computerized Tomographic Imaging" by A. C. Kak and
        Malcolm Slaney (IEEE Press, 1988).  It has nothing to do with my
        work at Apple.

	Programs included:
        back            Back Projection
        bgr             Insert Black Cross Hatch on the Comtal
        cen             Find the Center of CRC Scanner Data
        disn            Quantize an N x N picture
        filt            Filter Projection Data
        fmm             Find Minimum and Maximum of Data
        g128            Generate 128 x 128 Picture from Quadrants
        gen             Generate Simulated Data for CT Scanners
        hf              Homorphic Filter Waveforms
        hist            Find Histogram of Eight Bit Binary Data
        kakman          Print Help Files for CRC Tomography Software
        median          One Dimensional Median Filter
        merge           Add Two 128 x 128 Images together
        path            Generate multipath data
        pdsname         Extract PDS Name Information
        radon           Plot the Radon Space of the Scans
        scan            Massage Raw Data from the CRC Scanner
        sim             Simulate Ellipse Field Images
        tof             Calculate Time of Flight vs. Threshold Value.
        tv              Extract True Values from Comtal Images
        window          Convolve an image with a square window (averaging)

Hope this helps.
Doug Merritt				doug at netcom.com
Professional Wild-eyed Visionary	Member, Crusaders for a Better Tomorrow

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