Dendrites that look not connected

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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tcp

Dendrites that look not connected

Post by tcp » Thu Feb 14, 2013 6:51 am

Dear Forum,

I have imported (import3D) a reconstruction of a neuron.
Because the reconstruction had no soma I made one and I connected the emerged dendrites.
At the shape window, not all dendrites look connected to the neuron. When I call the topology function, the diagram is as it should be.
The signal is propagated through the seemingly unconnected dendrites.

Is there any need to take further action? How can I have something that will not only be right but look right?

Kind regards,
Eleftheria

ted
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Re: Dendrites that look not connected

Post by ted » Thu Feb 14, 2013 9:59 am

tcp wrote:Is there any need to take further action?
No. The facts that topology() shows the connections, and charge spreads throughout the cell, prove that the model is fully connected.
How can I have something that will not only be right but look right?
You might try eliminating any direct assignment to the soma's L or diam. Define its geometry with pt3d statements, and only with pt3d statements. Example: for a 10x10 um soma

Code: Select all

soma {
  pt3dadd( 0,0,0,10)
  pt3dadd(10,0,0,10)
}
Then make sure that all of the soma's child sections are connected to its 0 or 1 end, not to soma(0.5). Let me know if that helps.

tcp

Re: Dendrites that look not connected

Post by tcp » Sat Feb 16, 2013 3:19 pm

Thanks Ted,
Geometries were already defined by pt3dadd statements and connected to soma(0) or soma(1).

Hmm, should I just carry on?

Best,
Eleftheria

ted
Site Admin
Posts: 5218
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: Dendrites that look not connected

Post by ted » Sun Feb 17, 2013 11:14 am

It's just a cosmetic problem. However, if this is an important issue for you, I will have to be able to reproduce the problem myself--which means you should send the necessary code in a zip file to ted dot carnevale at yale dot edu.

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