Fiji- Weka Trainable Segmentation help

Once an image has been segmented into different classes, is there any way to separate the output into layers, each containing a different segment of the image?
This is my input image.
IMG_20190725_120924
Here is my output image:
filtered%20image
It is still a work in progress, but it should give an idea of what I am trying to do.
The colonies are segmented into 5 classes according to color. I want to be able to separate the image into a stack, so that each layer contains only one class. The goal is to use a colony counter plugin to count the number of colonies in each layer so we can easily determine how many colonies of each color are on the plate.
Is there any way to do this?
Thank you

@A.millepora

You can always process the output labels via MorphoLibJ’s label tools. That tool is also by the same developer as TWS, @iarganda. You don’t necessarily have to use the Colony Counter plugin to count your objects… using some simple Segmentation scripts should do the trick. Just check out these helpful links:

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