Sholl Analysis Radius Setting

Hi there.
I have some issues with Sholl Analysis of microglia cells. It started after the update of java so I can’t manage what’s going on. First of all, I have problem in setting radius size, because it doesn’t accept dots (e.g. 10.00 will not be accepted). I have tried with comas and I get this type of results/image

forum sholl.csv (30.5 KB)
From this results I can see that I have problems with the radius size. In ideal work there should be 5 radii (10, 20, 30, 40, 50) just as in pic
But during analysis something is going wrong and I cant find the matter. Please help

Thank you in advance for your help.


I believe @tferr would be the best person to assist you in this issue.

Too - perhaps sharing the input image and a list of all settings you are using in the plugin would also be helpful? That way we can attempt to reproduce your results…

Really sorry for the late reply. Just some clarifications: on your first image, your radius step size is set to continuous (that moire pattern stems from the fact that a sampling shell is being drawn at every pixel), presumably because the value you entered is perceived as non-numeric. As per why you cannot specify values is not clear to me, and I cannot reproduce it with the latest version 4.0.1 (so I will assume this is an old issue that has been meanwhile fixed). A couple of notes:

  • The number of decimal places you can specify is tethered to the precision of the voxel size that is stored in the image header (e.g., it does not make sense to allow 0.0001um steps if the pixel size is 0.50um)
  • If for whatever reason specifying values in the fields is giving you problems, you should still be able to use the adjustment sliders/spinners. Sending you a snapshot of a prompt in which all parameters were adjusted with sliders: