area calculation?

[ubartsch]

Hi,
I am building a 3 compartment model from a detailed morpholgical recontruction of a pyramidal cell.
The basic idea is to build compartments in typical length with a diam that keeps the membrane total area of the detailed model.

My question is how does the area() function calculate the area of a cylindrical segment?
If I build a single compartment with L=100 and a diam =10 area gives:

Code: Select all

area(.5)
        3141.5927

But the surface area of a cylinder with this dimensions should be 6911,5 um2! The shell only is 6283,1 um2.

The nrn help tells me the area fct uses numerical (trapezoidal rule) integration to integrate the effective (?) area of a compartment/segment?
What means effective then?
Either this integration seems to be pretty bad or I missed an essential point?!

Many thanks for a clarifying answer!

UB

[ted]

Here's a discussion of how model geometry is handled in NEURON--
file:///home/ted/ms/neuron/nrnhelp/help/neuron/neuron/geometry.html#Geometry
Reading down through the text, notice the following:

In the stylized specification, the shape model used for a section is a sequence
of right circular cylinders of length, L/nseg, with diameter given by the diam range
variable at the center of each segment. The area of a segment is PI*diam*L/nseg
(micron2) . . . Ends of cylinders are not counted in the area . . .

If you are dealing with detailed morphometric data, you may want to try
importing it, in all its gory detail, with the Import3D tool (available in recent
versions of NEURON--
Tools / Miscellaneous / Import3D
). Handles NeuroLucida, Eutectic, and SWC formats.

[ubartsch]

simple mistake:
the shell area of a cylinder with height 100 and diam 10 is of course 3141,592 um2!

[ted]

I wish I had a nickel for every simple mistake I ever made.