www.neuron.yale.edu

Hello,

I am trying to understand how swc code gets converted into hoc code after I import morphometric data from Neuromorpho.org and save it as a hoc file using CellBuilder. I'm confused about one thing: when points are connected in series in the swc code, how does the program decide when to create a new section (eg, a new dendrite)? Here is an example of part of an swc code:

35 3 9.25 3.19 2.15 0.431 1
36 3 11.91 8.19 2.15 0.469 35
37 3 13.16 11.47 2.15 0.469 36
38 3 14.82 13.96 6.23 0.469 37
39 3 17.66 14.72 10.65 0.391 38

In the first line here, a new dendrite has been created that is attached to the soma. But between lines 38 and 39, the hoc code indicated that a new dendrite had been created. Basically what I'm asking is, how are new sections of the same type (such as dendrites) specified for in swc code?

Also, I just want to confirm my understanding: in a section that contains many points, each with a specific diameter, does NEURON treat this as a single section with one recalculated diameter and one length?

Thanks so much in advance.

chels wrote:I am trying to understand how swc code gets converted into hoc code

The source code for the Import3D tool is in nrn/lib/hoc/import3d.hoc and in
nrn/lib/hoc/import3d/*.hoc

when points are connected in series in the swc code, how does the program decide when to create a new section

In each line, the first field is the "index" of that line and the last field is the index of the
parent of that line.

between lines 38 and 39, the hoc code indicated that a new dendrite had been created

The clue to why this happened is not in the example that you cite. However, elsewhere
in that swc file you will almost certainly find a second line whose last field contains 38
(i.e. line 38 has two children, hence is a branch point).

in a section that contains many points, each with a specific diameter, does NEURON treat this as a single section with one recalculated diameter and one length?

Only if nseg is 1. Change nseg and each segment will be assigned a diam that is calculated
from the pt3d data so that it has the appropriate surface area. Read 5.5.2 3-D specification
in The NEURON Book, or the relevant parts of
http://www.neuron.yale.edu/neuron/stati ... l#Geometry
or
Hines, M.L. and Carnevale, N.T. The NEURON simulation environment.
Neural Computation 9:1179-1209, 1997 (on-line version available from links at
http://www.neuron.yale.edu/neuron/bib/nrnpubs.html ).