Sholl analysis: restricting analysis to a hemisphere

Hi, I am new to this plugin and I am having trouble restricting the Sholl analysis to either the dendrites or the axons - it always processes the whole cell.
In the guide, it says to restrict by ‘by holding ⇧ Shift while using the Straight Line Selection Tool’ while selecting the focal point. However, there is no difference when I hold down shift and the program still analyses the entire cell. Am I missing something?

Thanks for your help.

Hi Anna, Welcome to Forum!

That option is working for me with v3.6.7. Here is a snapshot:

The “restrict to hemisphere” option is only available when the plugin detects an orthogonal line in the image, i.e., a line selection that is either perfectly horizontal or perfectly vertical. The Shift modifier description is straight up from the user guide: It is just a convenient way to force straight lines to have 0 / 90 degrees in ImageJ. In any case, you should be able to create horizontal and vertical line selections in multiple ways: by (steady) hand, through a macro or script, etc.

I encourage you to run the plugin on the File>Open Samples> ddaC Neuron (84K) image: that image is always opened with an horizontal line, so you can test the “restrict to hemisphere” option right away. It may be useful to check the “Overlay sampling shells” so you can see the actual arcs. If you tilt that line to e.g., 30 degrees, and re-run the plugin you will notice that the option will no longer be available.

NB: In principle, the plugin could allow hemispheres tilted by any angle, it is just I found it very hard to implement a simple user interface for it. The only things I could come up with were: 1) a crowded drop down menu with a huge list: "Hemisphere above line, below line, to the NE of line, NW of line, etc… ", or 2) a dedicated protractor-like tool to generate an arc selection. The 1st would be cumbersome to use, the second wouldn’t be macro recordable… So any good suggestions on this are more than welcome.


Hi. That makes sense and has solved the problem. Thanks for your help :slight_smile: