I am measuring leaf area index by taking canopy photos of radish plants growing in individual pots. I did not have issues with that in the two first sample points, but later, the leaves reached the pot edges and when I try to use “make binary” or “threshold” like as was doing, the white of edges pots merge with the leaves. I have been trying to change all parameters of “threshold” tool but i did not achieve it. I attached an example picture. Thank you for your help
Plant photography seems to be trending, I think you will find what you need (more advanced segmentation) in the following thread (SIOX, TWS).
But from the looks of your example image, your photography of these plants is far from standardized which makes applying a common segmentation operation to all your images far more challenging. Standardizing the angle of photography as well as lighting will make everything much easier. See the principles page for some basic advice on image acquisition.
A quick test using color threshold also did the trick: