Why my Sholl analysis only works if scale is in pixels?

I am trying to perform sholl analysis in neurons, after applying a threshold and creating a mask (figure1). However, the analysis doesn’t take into account all the sampled values from the mask (figure2).
Then, I tried to apply the plugin Robust Automatic Threshold Selection (RATS), which allowed me to obtain the correct sholl mask (figure3) but all the values are relative to pixel unit. If before the analysis I try to set the scale again to µm, it doesn’t work anymore.

Anyone with a tip how about to overcome this problem?

Thanks in advance.