k-means segmentation in 3D

[Alexandre Santos Abreu]

Hello!

I have 3D data from microcomputed tomography and i am interested in a  
plugin that uses a k-means segmentation algorithm in three dimensions on  
an image stack. I know the ij-plugins toolkit  
(http://ij-plugins.sourceforge.net/plugins/segmentation/k-means.html) but  
the segmentation only seems to work in two dimensions.

Can anybody help me out?

Thanks!

Alex

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[Jarek Sacha-2]

On 1/2/2013 10:35 AM, Alexandre Santos Abreu wrote:
> I have 3D data from microcomputed tomography and i am interested in a
> plugin that uses a k-means segmentation algorithm in three dimensions
> on an image stack. I know the ij-plugins toolkit
> (http://ij-plugins.sourceforge.net/plugins/segmentation/k-means.html)
> but the segmentation only seems to work in two dimensions.
>
> Can anybody help me out?
I added support for segmenting grey level 3D images to k-means plugin
<http://ij-plugins.sourceforge.net/plugins/segmentation/k-means.html>,
it will be released soon.

Jarek


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[Jarek Sacha-2]

On 1/6/2013 8:36 PM, Jarek wrote:

> On 1/2/2013 10:35 AM, Alexandre Santos Abreu wrote:
>> I have 3D data from microcomputed tomography and i am interested in a
>> plugin that uses a k-means segmentation algorithm in three dimensions
>> on an image stack. I know the ij-plugins toolkit
>> (http://ij-plugins.sourceforge.net/plugins/segmentation/k-means.html)
>> but the segmentation only seems to work in two dimensions.
>>
>> Can anybody help me out?
> I added support for segmenting grey level 3D images to k-means plugin
> <http://ij-plugins.sourceforge.net/plugins/segmentation/k-means.html>,
> it will be released soon.

Updated ij-plugins toolkit is now available. It includes support for
k-means clustering of 3D images.
https://sourceforge.net/projects/ij-plugins/files/ij-plugins_toolkit/v.1.7.0/ 


Jarek

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[McRender]

Hi Jarek

I hava a little remark concerning the switch to java 1.7 for your plugins. I'am using your kmeans3d plugin for segmenting some medical images which I do like to display in the 3d viewer afterwards. It seems that there is a problem with Java3D and Java 1.7 at the moment. You are not able to see anything in the 3d viewer if you switch to the Java 1.7 jre or jdk. I have managed to compile your plugins for the Java 1.6 platform and can now use both in combination. Consider this just as an information if some one else runs in the same problems like me.

[Shameem Sampath]

Hi McRender,
I am a knee surgeon, and am also interested in segmenting 3D medical images . Just knees in my case .
Do you have any experience in this field ?
Regards,
Shameem Sampath
www.MrSampath.com
[phone]

Sent from my iPhone

On 23 Jan 2013, at 09:06, McRender <[hidden email]> wrote:

> Hi Jarek
>
> I hava a little remark concerning the switch to java 1.7 for your plugins.
> I'am using your kmeans3d plugin for segmenting some medical images which I
> do like to display in the 3d viewer afterwards. It seems that there is a
> problem with Java3D and Java 1.7 at the moment. You are not able to see
> anything in the 3d viewer if you switch to the Java 1.7 jre or jdk. I have
> managed to compile your plugins for the Java 1.6 platform and can now use
> both in combination. Consider this just as an information if some one else
> runs in the same problems like me.
>
>
>
> --
> View this message in context: http://imagej.1557.n6.nabble.com/k-means-segmentation-in-3D-tp5001302p5001503.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

... [show rest of quote]

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[Jarek Sacha-3]

On 1/23/2013 4:06 AM, McRender wrote:
> I hava a little remark concerning the switch to java 1.7 for your plugins.
> I'am using your kmeans3d plugin for segmenting some medical images which I
> do like to display in the 3d viewer afterwards. It seems that there is a
> problem with Java3D and Java 1.7 at the moment. You are not able to see
> anything in the 3d viewer if you switch to the Java 1.7 jre or jdk. I have
> managed to compile your plugins for the Java 1.6 platform and can now use
> both in combination. Consider this just as an information if some one else
> runs in the same problems like me.
Sorry for the inconvenience. I am using 3D viewer on 1.7 with no
problems. Did not realized that there were issues. What OS are you
running? Are you using Fiji? I had some problems with Fiji, 3D viewer,
and 1.7 in the past.

Jarek

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[McRender]

You are right. I'am using Fiji on 64 bit Windows 7 & 8. I'll check your plugin again with a clean installation of ImageJ and the 3d Viewer plugin...

Steph