I want to create a macro running "Analyse Particles" on different images. The problem is that I have to Color Threshold before running the Analyse command. The generated macro using the "Macro" button does not work correctly, it generates a binary image, therefore the values Skew, Curt, Mean, StdDev, etc are useless.
My images are already preprocessed, so the required threshold settings are pretty simple.
The Threshold Color plugin internally converts your RGB image to the HSB color space, so you can't interactively use Analyze Particles because there is no single threshold value set.
You should indeed generate the binary image, and then use the "Redirect to" option in Set Measurements to measure on your original image.
Please also see the user guide and several discussions about color analysis on the ImageJ forum.
But if you already pre-process the images, why don't you make them 8-bit gray scale? That would simplify the measurements and save memory and/or processing time.
