Weka segmentation plugin

Hey all,
Any idea how I can train the weka segmentation plugin to separate cells that are touching?
The images Im working with as follows:

The ones I’m trying to separate are the ones that are touching

Here is the result of the overlay after training the classifier, see the long red blob that the touching cells produce, I need a way to break that into the individual cells.

I would recommend choosing areas slightly close to your cells as part of your background training. That should tighten the red areas and make for easier separation with the next step.

After the pixel classifier have you performed a watershed separation? This post mentioned using a watershed plugin.

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