[Insight-users] 3D Watershed segmentation speed

[Gaetan Lehmann]

Hi,

Just to be sure: What do you call too slow ? Can you give an execution  
time ?
Have you build the project is Release mode ?

Gaetan

On Wed, 07 Jun 2006 11:00:03 +0200, Kalle Pahajoki <kalpaha at st.jyu.fi>  
wrote:

> Hi
>
> I'm developing a tool based on the watershed segmentation for the  
> segmentation of 3D confocal microscopy images, and so far it seems to be  
> very suitable for my purposes. The problem with the method is it's  
> speed: images I'm working with are typically in range  of512x512x24 -  
> 1024x1024x24 voxels. For these images, the method is too slow to be  
> usable.
>
> So far I haven't had the patience to run the method on a full sized  
> dataset (because I'm working on the software, and not producing any  
> meaningful results) but always resorted to scaling the dataset to the  
> range 128x128x24. For the actual users, however, I cannot really justify  
> this kind of loss of information.
>
> I've usually used the VTK hybrid 2D median for the filtering (since the  
> anisotropic diffusion recommended in the ITK book is slow as well  
> *grin*). I usually test with Threshold = 0.01 and Level = 0.2. Could  
> there be significant speed gains in tweaking the parameters or filtering?
>
> In general, is there any way to speed the method, other than resampling  
> the datasets to a smaller size?
>
> Some software used here (e.g. 3D for LSM by Zeiss) offer a similiar  
> method with almost interactive speeds (or at least speeds that the users  
> can accept). Do they employ a fundamentally different technique?
>
> Kalle
>
>
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-- 
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
http://voxel.jouy.inra.fr