[Insight-users] Segmentation of microscopic vascular images

[Gib Bogle]

Hi Badri,

Very droll - "you may be interested" - your paper hits the bullseye!  I will now 
attempt to understand it.

Many thanks.

Best regards
Gib

Dr. Gib Bogle
Senior Research Fellow
Auckland Bioengineering Institute
University of Auckland
New Zealand

http://www.bioeng.auckland.ac.nz

g.bogle at auckland.ac.nz
(64-9) 373-7599 Ext. 87030

On 22/12/2010 10:12 a.m., Roysam, Badri wrote:
> Gib,
>
> You may be interested in this paper:
>
> 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.
>
>
>
> 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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>