[Insight-users] 3D watershed segmentation

[Luis Ibanez]

Hi Marco,

The Watershed filter will work with N-Dimensional images.

You will find a 3D example of watersheds in the file:

      Insight/Examples/Segmentation/
                       WatershedSegmentation2.cxx

(Please note the "Dimension = 3 " statement in line 58).


This code runs straight forward on 3D images.

For example, if you run it in the BrainWeb images

http://public.kitware.com/pub/itk/Data/BrainWeb/

with the following parameters:

WatershedSegmentation2
    brainweb165a10f17.mha  output2.mhd  0.01  0.15

(in a single line)

You will get a good initial segmentation of the
White matter and the ventricles.

This takes 50 seconds to run in a laptop with
an Intel T9600 processor @ 2.80GHz.
running Ubuntu 9.10, compiled with gcc 4.4
for Release.

----

If you want to get larger structures, then you should
use a water level higher than 0.15. Correspondingly,
if you want to get finer structures, then you should
use a water level lower than 0.15.

----

If you want to use seeds & watersheds, you
should look at the following paper in the
Insight Journal:

http://www.insight-journal.org/browse/publication/92
http://hdl.handle.net/1926/202
"The watershed transform in ITK -
discussion and new developments"
Beare R., Lehmann G.



The code of this paper is now available under


Insight/Code/Review/
itkMorphologicalWatershedFromMarkersImageFilter.h
itkMorphologicalWatershedFromMarkersImageFilter.txx
itkMorphologicalWatershedImageFilter.h
itkMorphologicalWatershedImageFilter.txx


For other "seed-based" segmentation algorithms,
please look at:

* Region Growing methods
** ConfidenceConnected
** ConnectedThreshold
** IsolatedConnected

* LevelSet methods
** FastMarchingLevelSetFilter

You will find all the above filters described
in detail in the ITK Software Guide:

   http://www.itk.org/ItkSoftwareGuide.pdf


Please read the "Image Segmentation"
chapter.


         Regards,


               Luis


---------------------------------------------------------
On Fri, Mar 26, 2010 at 5:52 AM, Marco Gheza
<marcogheza4mailinglists at gmail.com> wrote:
> Hi,
> I'm trying to create an itk software for 3D watershed segmentation of
> medical image. I'm working with vtk volumes. I tried the watershed example
> founded in itk-examples but I'm not able to use it with 3D images. Do you
> know how to modify the code? I changed 2 with 3 where I have to indicate the
> dimension but it didn't work.
>
> Another thing: does anyone already modified that code in order to be able to
> insert seeds or different region of interest? I'm desperately searching for
> a 3D segmentation software that works fine and accepts seeds (I accept every
> type of algorithm, not only watershed).
>
> Please help me, bye,
>
> Marco
>
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