[Insight-users] Level set segmentation parameters to anisotropic images

[BOURGEOIS Loic]

Hi Luis,

Thanks for your suggestion, I have decided to use "GeoInterp: Contour Interpolation with Geodesic Snakes
http://www.insight-journal.org/midas/view_item.php?itemid=512" adapted to my problem. I put the distance map (Danielsson) of my pre-segmented object instead of Fast-Marching as the initial level set but the output level set of the geodesic filter is the same of the input.
Am I missing something?

Regards,

Loic

-----Message d'origine-----
De : Luis Ibanez [mailto:luis.ibanez at kitware.com]
Envoyé : lundi 12 mai 2008 18:43
À : BOURGEOIS Loic; Insight Users
Objet : Re: Level set segmentation parameters to anisotropic images



Hi Loic,

                    Welcome to ITK !

It is hard to tell if the anisotropy of your MET images
would prevent LevelSet methods from running well.


I would expect that an anisotropy larger than 1:5
will make hard for level sets to behave properly.
However... this also depends on the actual content
of your image...


---

What I would suggest is for you to try the SNAP application.

   You can download binaries from http://www.itksnap.org/

or build it from the version in InsightApplications.

SNAP is build on top of ITK and provides a nice interface
for using LevelSets.

Another application that may be useful is Slicer:

     http://www.na-mic.org/Slicer/Download/Snapshots/


---

By testing your images with these applications will get
a feeling of whether the anisotropy is too large for the
LevelSets to work properly.

Please note that ITK LevelSet can be run by turning the
consideration of the spacing ON and OFF.

You may want to use them with using the spacing ON.

Also, a quick experiment that will help you see the
influence of anisotropy is to run the GradientMagnitude
RecursiveGaussianImagefilter in your image, and then
visualizing the image with slice orthogonal to the
plan of acquisition.

E.g. using a plane XZ, where Z is the direction with
the largest spacing. In this way you should see
rectangular pixels, and how they may have affected
the gradients of the image.


Please let us know what you find,



     Thanks


        Luis


----------------------
BOURGEOIS Loic wrote:
> Hello Mr. Ibanez,
> 
> I am new in this mailing list. I have to segment MET 3D (Microscopy 
> Electron Tomography) images which are very anisotropic : contrast is 
> quite good along x and y axis but is very low along z axis. So the issue 
> is to tune different parameters to the level set (geodesic) between x 
> and y axis, and z axis. Is there possible?
> 
> Regards,
> 
> Loic Bourgeois
> 
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Ce message (et toutes ses pièces jointes éventuelles) est confidentiel et établi à l'intention exclusive de ses destinataires. Toute utilisation de ce message non conforme à sa destination, toute diffusion ou toute publication, totale ou partielle, est interdite, sauf autorisation expresse. L'IFP décline toute responsabilité au titre de ce message.

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Visitez notre site Web / Visit our web site : http://www.ifp.fr
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