Sholl analysis/exporting trace files



I am trying to find a way to automate the tracing of SCG cells for Sholl analysis, where crossings of the neuron’s skeleton with concentric circles radiating from the cell body are measured to determine the extent of branching. I looked around a bit on the website and have built a pipeline to trace neurons, but I realized that CellProfiler doesn’t have the capabilities to do a Sholl Analysis on its own (I realized I ran into some of the same issues as the author of this thread Trying to trace neurites within a limited radius of an object). Here’s an example image of the cells I would like to trace.

I wanted then to be able to export the skeleton files I created for use in another program since this program makes the tracing process much easier and quicker, but haven’t been able to find a good way to do this. When I try to save a skeletonized image as a png, I have to zoom into a particular region of the image to get a usable resolution, otherwise the skeleton is broken and segmented in the exported file. Is there any way to export a high resolution image from the output of the skeletonize function without having to crop my image by zooming? I’ve attached some of the images I have exported both zoomed in and zoomed out for comparison. I appreciate the help greatly!



Hi Kenny,

Automated, full resolution exporting of the graph image is on our to do list and will hopefully be included in our next release. Stay tuned!


Oh that’s great to hear, thank you for the quick reply!