Working with .loc() and segments

[kirkw-1]

Couple of questions regarding how .loc() and segments work together:

1. Is a stimulus at   cell.soma.loc(1.0).stimulate(current)    identical to one at   cell.soma.loc(0.5).stimulate(current)   given a single segment soma with non-zero size?  I had thought we could use .loc() but the source code seems to indicate that the stimulus is placed simply at the "segment/compartment" rather than locations within the compartment.  And if so, which 'location' should we take as the default.  I ask this because my dendrite is connected to one end of the soma, and stimulus for a test I'm doing per original HOC model would be at the exact same place where the dendrite joins the soma so I wanted to place the stimulus at loc(1.0).

2. Similar question, given   distance_pathwise(cell.soma.loc(1.0), cell)    the source code and disjkstra within nx seem to work similarly on segments/compartments, rather than locations within segments, is that right?  And so should I assume the distance_pathwise is not actually from loc(1.0). but rather from loc(0.5)?   And the target points, would that be the loc(0.5) of the target segment? And is it possible to vary that?

Thanks for your help,
Kirk

[michaeldeistler]

Hi Kirk, sorry for the late reply!

Is a stimulus at cell.soma.loc(1.0).stimulate(current) identical to one at cell.soma.loc(0.5).stimulate(current) given a single segment soma with non-zero size?

Yes, they are identical. Jaxley only allows insertion of stimuli into compartments, not "in between".

nx seem to work similarly on segments/compartments, rather than locations within segments, is that right?

Yes, that is also right.

And so should I assume the distance_pathwise is not actually from loc(1.0). but rather from loc(0.5)?

For a one-compartment branch, they are identically. If there are more than one compartment per branch than they will differ.

We currently have no way of modifying the behavior here, but we will consider it for future versions.

Hope that helps!
Michael