I am new to imageJ and I would like to use the (amazing) Trainable Weka Segmentation plugin to quantifiy the total area of red and green pixels, compared to the background in each picture (similar to this example Quantifing Weka Output).
My red and green pixels are sediment particles covered with fluorescent pigment, photographed under UV light.
I managed to train the classifier on a stack of croped images by choosing “Gaussian blur” and “Difference of gaussians” but it’s quite difficult to understand what all the segmentation settings do (also after reading the wiki pages http://imagej.net/Trainable_Weka_Segmentation).
Can someone recommend improved sementation settings for my pictures? Here https://www.dropbox.com/sh/8ffai020jppk1s9/AADhcVBgsxUOyn6qdsQj77GEa?dl=0 are examples and segmentation results of the first three pictures. I also added the classifyer.
Thanks for any advice!