[Insight-users] Image or Mesh to Tubes

[Ghassan Hamarneh]

This did not make it to the list:
=================
Date: Tue, 1 Aug 2006 07:36:18 -0700 (PDT)
From: Ghassan Hamarneh <hamarneh---at---cs.sfu.ca>
To: Kevin H. Hobbs <hobbsk at ohiou.edu>
Subject: Re: Fwd: [Insight-users] Image or Mesh to Tubes


Hello Kevin,

You may be interested in these two publications by our group on segmenting
and analyzing tubular structures (and branchings/children in the first
paper).

C. McIntosh and G. Hamarneh, "Vessel Crawlers: 3D Physically-based
Deformable Organisms for Segmentation and Analysis of Tubular Structures
in Medical Images", IEEE Conference on Computer Vision and Pattern
Recognition, 2006, pp. 1084 - 1091.

http://www.cs.sfu.ca/~hamarneh/ecopy/cvpr2006.pdf

C. McIntosh, G. Hamarneh, "Spinal Crawlers": Deformable Organisms for
Spinal Cord Segmentation and Analysis", MICCAI, 2006.

http://www.cs.sfu.ca/~hamarneh/ecopy/miccai2006.pdf

We have also submitted the ITK-deformable organisms framework to insight
journal and MICCAI workshop on open science:

http://hdl.handle.net/1926/228
=================

On 8/2/06, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>
>
> Hi Kevin,
>
> You are right,
>
> TubeSpatial objects can provide a natural representation for
> dentrites in neurons, and it will be more efficient and meaningful
> than a mesh around the surface.
>
> You may want to get in touch with Julien Jomier and Stephen Aylward
> (cc in this email). They developed most of the Spatial Objects hierarchy
> in ITK, and they have been working in using the TubeSpatialObject for
> representing vascular trees by doing Model-to-Image registration.
>
> As you pointed out, the concept of children fits very naturally as
> a representation of the branching partition in a tree structure.
>
> For some background on Model-to-Image registration, you may want to
> look at the final section of the Image Registration chapter in the
> ITK Software Guide
>
>
>        http://www.itk.org/ItkSoftwareGuide.pdf
>
>
>
>    Regards,
>
>
>       Luis
>
>
> -------------------------
> Kevin H. Hobbs wrote:
> > I've been working with confocal images of neurons. It strikes me that
> > the tube spatial object might be the best representation for the
> > dendritic tree.
> >
> > Center-lines and radii seem more memory efficient than a full surface
> > mesh for something that's tube-like.
> >
> > The representation seems very similar to the representation in Neuron
> > ( http://www.neuron.yale.edu/neuron/ ) so conversion might be possible
> > allowing for simulations.
> >
> > The idea of children might allow for studying the branching pattern more
> > directly than does the surface mesh.
> >
> > What I do not see is any way to automatically place tubes based on image
> > or mesh data. Is anybody working on automatically placing tubes?
> >
> >
> > ------------------------------------------------------------------------
> >
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> > Insight-users at itk.org
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>
>
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