as part of my phd, I decided to analyze differences in bird eggshell color patterns and so I took some photos (.RAW) of these.
Firstly, I tried to isolate the pigmented part (‘spots’) from the background of the eggshell but I found some problems. I created a ROI to isolate the egg from the total image, then I converted the obtained picture to 16bit in order to apply the threshold (I tried to used ‘Autothreshold’ plugin). I chose the Shanbhag method that is the most represented for the initial spot pattern image. On this image I used the tool ‘Analyze particles’ (size pixel = 0-infinity) to automatically mark the spots. By this way, I thought that I was able to compare the pigmented area on the total area (px unit). However, this method was not able to mark all the pigmented area but only a part of these.
Please, could you suggest me another method because I’m not sure that ‘my method’ is not the best one?
Furthermore, in order to avoid any aberrant parts on the image of the eggshell surface caused by the curvature of the eggs (e.g. shaded parts), I would like to know if there is a way to reduced my egg ROI of a standardized way, could someone help me?
I attached my photo as example (sorry, here my photo is in jpeg).
Thanks to all in advanced.