How do I upload the tiff and trace files? According to this site, I am not allowed to upload tiff files via messages.
I apologize for the confusion! The principal investigator is interested in determining if there are layer differences in neurons. To determine if there is a difference, the total length within that layer is needed (which is why I use NeuronStudio to retrieve the lengths within each Sholl shell). Based on his experience, the SR stratum is approximately 200-250 um away from the soma; the rest of the dendrite endings are considered the SLM stratum.
To separate the two strata, I used the straight line function from the middle of the soma to approximately 250 um away from the soma. I assumed the Sholl analysis utilizes the 2D tracing for analysis because each shell is a certain radius (we use a radius of 10). For many of the tracings, the total radius (which ranges from 300-420) of the Sholl analysis is equivalent to the line I draw from the soma to the end of the dendrite. There are a few that have Sholl shells beyond the end of the tracing that contain lengths and intersections, which is why I am confused. It is possible the poor quality of the images are causing the issue. Thank you!