I’m not quite sure if this is the right place to ask this, but since I want to use FiJi for analyzing an image I start here.
As stated in the thread topic, I want to locate the position of an valley within a line selection profile of an image.
You can clearly see a dark shadow in the OCT picture (optical coherence tomography). I want to know the approximate location of the “shadow” area in order to crop the picture to the bounds of this area.
My approach was to extract a profile of an horizontal line and then analyze the profile.
run("Median...", "radius=10"); // reduce noise makeLine(0, 0.40*getHeight(), getWidth(), 0.40*getHeight()) / profile = getProfile(); Plot.create("Line Profile", "Pixel", "Grey-Value", profile) maxLocs = Array.findMaxima(profile, 10); Array.show(maxLocs);
But I have trouble to detect the right maxima (or minima for that matter) to get the positions.
Do you have any suggestions how I might be able to detect my desired area? I have to do this on a couple of hundreds of pictures, hence the approach with a macro code.
Any help would be appreciated.
If you have any questions, don’t hesitate to ask
btw. the image shows a bovine enamel/dentin block with an artificial lesion, which I want to analyze further