[Insight-users] Segmentation of microscopic vascular images

[Roysam, Badri]

Hello Gib,

You may be interested in this paper that addresses exactly your problem:

Arunachalam Narayanaswamy, Saritha Dwarakapuram, Christopher
S. Bjornsson, Barbara M. Cutler, William Shain, Badrinath Roysam, Robust
Adaptive 3-D Segmentation of Vessel Laminae from Fluorescence Confocal
Microscope Images & Parallel GPU Implementation, 29(3):583-97, IEEE
Transactions on Medical Imaging, March 2010.

Code is also freely available.

Badri Roysam, D.Sc.
Hugh and Lillie Cranz Cullen University Professor
Chair, Electrical & Computer Engineering
N325, Engineering Building 1
University of Houston
Houston, Texas 77204-4005
Phone: 713-743-1773/4435
Fax:  713-743-4444
Email: broysam at central.uh.edu


On 12/21/10 2:35 PM, "Gib Bogle" <g.bogle at auckland.ac.nz> wrote:

>Hi,
>
>Our stack of vascular images was obtained by fluorescent staining and
>multi-photon microscopy (on a mouse lymph node).  The significant
>difference 
>from the CT and MRI data that are the usual starting point is that in our
>case 
>only the inside surface of the vessels is visible.  In other words, the
>stack 
>contains empty tubes with very thin walls - the interior of the tubes
>having the 
>same intensity as the exterior.  This means that the usual level set
>approach to 
>segmentation will not work directly.  If the tubes had no holes the
>"snake 
>evolution" method of ITK-snap would work fine, but variability in stain
>intensity gives rise to many leaks.  What is needed is a "tube healing"
>step in 
>which holes in the tube wall are patched.
>
>I have some ideas about how to approach this, but since it's quite tricky
>and 
>likely to be time-consuming I thought I should check first to see if
>anyone has 
>done something similar, or if there are existing methods in ITK that
>could be 
>employed.  What's needed is a kind of focussed dilation procedure.  The
>edge of 
>a hole needs to grow in the plane tangential to the nearby tube wall.
>
>Any suggestions?
>
>Thanks
>Gib
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