Sholl Analysis Help




I am trying to perform a Sholl Analysis and when I am I looking at the image, I just see rainbows of circles, not concentric circles around the neuron.

I imported an swc file from NeuTube and then did my sholl Analysis. I am not sure what exactly is this issue here. Thanks.


Hello! Is anyone able to help me with this? I have been trying but I am still getting the same set of circles


@tferr is the best person to help you I think… Personally - I am not well-versed in Sholl… but let’s see if Tiago can help you.

eta :slight_smile:


Hi @Ary,

This is detailed in the Sholl Image section of SNT’s documentation:

In short, that left-sided image only carries the intersection labels. Such labels still need to be applied to the surface reconstructions of the legacy 3D Viewer. You can do so using the ‘Use colors/labels’ dropdown-menu of SNT’s main dialog.

BTW: In the SNT pre-release version that option allows you to apply labels from any saved image. It has been renamed “Apply Color Labels” and has been moved to the “3D tab” of the main prompt. And


Hello I tried to do it again but I couldn’t find the drop-down menu you were talking about? Where is it on here?


It is the 3D Viewer: Use colors / labels from menu in your snapshot. It is disabled in your case because you seem to be using a 2D Image. Traditionally 3D related commands are automatically disabled in SNT when no 3D image is found. If I recall correctly, I’ve removed such restrictions in the IJ2 rewrite (yet to be released). If you want to render 2D traces in the 3D Viewer (Is this really what you are trying to do?), then subscribe to the Neuroanatomy update site and run the pre-release version using Plugins>Tracing>Simple Neurite Tracer


Hm. Alright. I thought my image was 3D as I am able to open it in the 3D Viewer. When I enable the 3D Viewer I still get the same image and don’t seem to be able to change it. Would I still need to do what you said above? Do you know if there is another program I could use for the Sholl Analysis?


Why can’t you? The drop-down menu to choose the labels image from is not disabled in your screenshot. Did you click on it? 1) Do click on it: it will be populated by a list of all images currently opened by ImageJ, 2) Choose the Sholl analysis of all paths for Fusedsuraj.tif, 3) the labels of the chosen image will be immediately applyed to volume being displayed in the 3D viewer (note that the GUI may be unresponsive while this operation takes place).

You seem to be convinced the program is not working, but your screenshots seem to say otherwise so there seems to be some misconception here.

The documentation links above were not useful? The Sholl image is a labelled mask of the analysis. The fact that the program is displaying it means it already analyzed the traces. Even if this particular feature would not be working for you (it seems to work as expected in an up-to-date ‘vanilla’ Fiji installation), the analysis would complete neverthess.

Please go ahead and press the “Analyze Profile”, “Preview Plot” and “Save Profile…” buttons next to the “Sholl Image” button that you have been pressing so far and get acquainted to the plugin. If something is not clear after reading the documentation, please do let us know, and we’ll try to make the software more intuitive.

If you want to access the latest improvements of the plugin, yes. The next release of SNT introduces several improvements that may not be compatible with existing workflows. So the most appropriate way to allow users to experiment the new features is through an opt-in mechanism). Note that the effort on your part is minimal:

  1. Run Help>Update…
  2. Press Manage Update Sites and check the “Neuroanatomy checkbox”
  3. Restart and run Plugins>Tracing>Simple Neurite Tracer…