Importing 3D data: number of sections

Managing anatomically complex model cells with the CellBuilder. Importing morphometric data with NEURON's Import3D tool or Robert Cannon's CVAPP. Where to find detailed morphometric data.
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luciana
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Importing 3D data: number of sections

Post by luciana » Mon Jan 12, 2015 2:48 pm

Hello!

I imported a neurolucida file (.asc) to NEURON. The dendritic tree was pooled into 56 sections, but I would prefer more sections containing less vectors (hopefully around 100) in order to be able to discriminate within branches. More specifically, I would like to insert different conductances within a portion of the dendrite.
What are the criteria NEURON uses for pooling vectors into sections and is there any way to modify it?

Thank you in advance.

ted
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Re: Importing 3D data: number of sections

Post by ted » Tue Jan 13, 2015 1:36 pm

You may think of NEURON's Import3D tool as treating each branch point in a morhpometric data file as the termination of a neurite and the origin of one or more child neurites. If you have access to NeuroLucida's software, you might want to experiment to see what happens if you discretize a single neurite as if it were the series connection of two or three neurites. However, even if that works, it could be very tedious to manually insert branch points along the lenght of individual neurites.
luciana wrote:I would prefer more sections containing less vectors (hopefully around 100) in order to be able to discriminate within branches. More specifically, I would like to insert different conductances within a portion of the dendrite.
You could simply increase nseg, then specify different conductance densities along each neurite as necessary. If you use the CellBuilder to manage your imported morphologies, it is very easy to take advantage of the d_X discretization strategy to ensure that all segments are shorter than a user-specified maximum length. Or you could accomplish the same result by executing the following code after your model's basic anatomy has been set up:

Code: Select all

proc geom_nseg() {
   forsec all { nseg = int((L/$1 + .999)/2)*2 + 1  }
}
geom_nseg(50) // choose odd nseg so that no segment is longer than 50 um
If you prefer some other maximum segment length than 50 um, just change the argument to geom_nseg().

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