www.neuron.yale.edu

I have a hoc code to read a data file containing the morphometric details of a cell.

There is information about the center and diameter for the soma. However, in order to create the cell body, I had to only use the diameter. When viewed using "Shape plot" the soma is shown as a line.

My question is that I have more than a few branches arising from the cell body all along its circumference. How in Neuron should I get the different branches to connect to the respective coordinates along the cell body, which is now a line rather than a sphere (or a circle)? Do I have to make multiple segments in soma based on the number of branches from the cell body and connect them to respective segments?

Is there a way to render the soma as a sphere or circle?

Multiple questions here, so multiple answers.

mani wrote:I have a hoc code to read a data file containing the morphometric details of a cell.

There is information about the center and diameter for the soma. However, in order to create the cell body, I had to only use the diameter.

For maximum control over the appearance of a model cell, specify its
geometry with pt3d statements--see
http://www.neuron.yale.edu/neuron/stati ... metry.html

If you want your model soma to have the same surface area as that
of a sphere with diameter d, just use a pair of pt3dadd statements to
make a cylindrical section with diameter = length = d.

When viewed using "Shape plot" the soma is shown as a line.

That's how it will look unless you tell the shape plot to use the
Show diam style (bring up graph menu, select Shape style, and then
choose Show diam).

My question is that I have more than a few branches arising from the cell body all along its circumference. How in Neuron should I get the different branches to connect to the respective coordinates along the cell body, which is now a line rather than a sphere (or a circle)?

If you want to control where the child sections are drawn on the
screen, use pt3dstyle (see
http://www.neuron.yale.edu/neuron/stati ... #pt3dstyle
). Note that this will have _absolutely_ no effect on simulation results; it
just makes the shape plot less disturbing to anatomists (connecting the
sections to the midpoint of the soma would otherwise result in a shape
plot that shows all child sections arising from the very middle of the
soma).

Do I have to make multiple segments in soma based on the number of branches from the cell body and connect them to respective segments?

No. nseg can be 1.

Is there a way to render the soma as a sphere or circle?

No. It is possible to approximate a spherical outline by using a
sequence of pt3dadd statements to produce a shape whose diameter
varies in a way that looks more or less circular. However, do not
set diameter at either end to 0, or you will find that child branches
attached to the 0 or 1 end will be isolated from the soma by an
effectively infinite resistance.