Hi! I’m new to ImageJ and Fiji, and am having trouble figuring out how to effectively create masks and measure ROIs.
For example, I would like to be able to draw selections on the following image and calculate measurements for each ROI without include information from the white and dark circular objects.
I’ve used the Trainable Weka Segmentation plugin to classify the objects already-- the region in the original image corresponding to green is what I would like to calculate measurements for.
From here, what is the best way to create a mask that excludes what we see in purple and red; and take intensity measurements that exclude information from those objects? And is this the best way to complete this task in Image J? I’ve already binarized the classification output using the color threshold function, but am a bit lost as to where to go from here.
Also as an aside, is there a way to properly run the Weka Segmentation on very large images?