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I am trying to use the spot segmentation plugin on an image the I have but whenever I carry out the plugin it picks up a lot of the background noise and I end up with the box with grey segments, where the large segments are what I'm interested in and the smaller segments in the background are not. Any help with the variables that I need to change would be appreciated.

** The image shows the local maxima filter, the original image, spots segmentation settings panel and the segmentation product

enter image description here

Martin Evans
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Zaid Malhees
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  • Did you read http://imagej.net/Segmentation ? Did you try the [TWS plugin](http://imagej.net/TWS)? Can you post the original data somewhere, instead of just a screenshot of your attempts? – ctrueden Jun 30 '15 at 17:47
  • It says weka is for 2D only, and the images i'm working with are 3D. I can post the original image which I would like to segment (it's a stack of 50 slides) – Zaid Malhees Jul 06 '15 at 01:38
  • TWS can process 3D data a slice at a time. It just won't segment 3D objects right now. I believe that is planned for the future though. – ctrueden Jul 07 '15 at 20:21

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