Cases like this it is always best to upload some images as example…
Also go easy on the acronyms: SLM and SR may not mean much to extremely talented people outside the Neurosciences that have the expertise to help you out.
As a rule of thumb: Only well-thought questions can have well-thought answers!
Anyway, I think I understood your two questions, so I will rewrite the first one here for clarity:
Question 1: I have a (traced) neuron, and would like to restrict the measurements of my traced paths to confined regions, defined by histologically-defined boundaries, such as in this neurolex example (in which the traced the neuron appears in filled lines, and histological layers (labeled in latin) are highlighted by dashed lines).
How can it be done?
(NB:I am using Simple Neurite Tracer (SNT) and an updated Fiji installation subscribed to the Java8 updated site.)
You would trace your neuron AND also trace the boundaries of the layers of interest (exactly as in that neurolex example). You could either store the traces for the layers on the same file containing the neuronal traces, or on a separate file. Then, you would need to write a script that would loop for all the traced points in the neuron and monitor their location relatively to the traced boundaries.
If you don’t want to script your way out of this problem, than you could try the “ImageJ” way:
- Trace your neuron, and in SNT obtain its skeletonized image using the Make Line Stack command
- Trace your layers and obtain their skeletonized image as in 1. Do some processing so that your layers become filled regions
- Use the logical operators in Process>Image Calculator to extract the voxels of image 1 that contained by the image 2 mask
- Then use Analyze>Skeleton to measure the result
Let us know if something is not clear. Now for your second question:
The answer is similar to the one above: You would need a script (BTW, I would be quite surprised if something does not already exist, e.g., for Neuron), or use a similar approach as the one described above. Just this time, skeletonized paths would need to be filtered by annular masks. Let us know if you need help with the latter.
I’ve added a new issue for this If people think this is an important feature. But I have to say I won’t have much time to work on it any time soon.
BTW, I wanted to mention that it will be soon possible to run the Sholl Analysis plugin on SNT traces directly, and vice-versa run the Sholl Analysis plugin from within SNT.